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<TD class="DocTitleText" align="left">Molecular Modeling Database (MMDB) Help</TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../mmdb.shtml"> OVERVIEW </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="mmdb_search.html"> SEARCH </A></TD>
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<P class="indent20bottomspace">This help document provides detailed descriptions of the <A HREF="/structure/"><B>Entrez Structure</B></A> database content, search system,<BR>and display formats. The "<a href="mmdb_how_to.html"><B>How To</B></a>" page provides <a href="mmdb_how_to.html"><B>quick start guides</B></a> for some common types of searches.<BR>Once records of interest are retrieved, follow Entrez's "Links" to <a href="../../structure_discover.html"><B>discover associations among previously disparate data</B></A>. The <A HREF="/books/NBK3837/"><B>Entrez Help</B> document</A> provides additional information about the search system and the databases it can be used to search.</P></TD>
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<!-- ==================== TOC_TABLE_OF_CONTENTS ================= -->
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<TD ALIGN="left" VALIGN="TOP" class="WhiteCell" style="white-space: nowrap;">DETAILED TABLE OF CONTENTS</TD>
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<TD ALIGN="left" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;">DETAILED TABLE OF CONTENTS</TD>
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</TR>
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</TABLE -->
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DETAILED TABLE OF CONTENTS
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<A NAME="TOCWhatIs"></A>
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<UL>
|
||
<LI><A HREF="#WhatIs">What are <B>macromolecular structures</B>?</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#FourLevelsOfStructure">Four levels of protein structure (primary, secondary, tertiary, quaternary)</A></LI>
|
||
<LI><A HREF="#ExperimentalMethods">Experimental methods (X-ray crystallography, NMR)</A></LI>
|
||
<!-- UL>
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||
<LI><A HREF="#ExperimentalMethodsXray">X-ray crystallography</A></LI>
|
||
<LI><A HREF="#ExperimentalMethodsNMR">Nuclear Magnetic Resonance (NMR) spectroscopy</A></LI>
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||
</UL -->
|
||
<LI><A HREF="#DatabaseApplications"><B>How can 3D structures be used to learn more about proteins and other biomolecules?</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DatabaseApplicationsRepresentativeStructures">identify representative 3D structures for protein families</A></LI>
|
||
<LI><A HREF="#DatabaseApplicationsSequenceStructureFunction">examine sequence-structure-function relationships</A> <I>(<!-- A HREF="#DatabaseApplications" --><A HREF="#SequenceStructureFunctionIllustration"><span style="color:#d70000">illustrated example</span></A>)</I></LI>
|
||
<!-- LI><A HREF="#DatabaseApplicationsStructureFunctionRelationships">reveal structure-function relationships</A></LI -->
|
||
<LI><A HREF="#DatabaseApplicationsConservedCoreMotifs">view 3D structures of conserved core motifs</A></LI>
|
||
<LI><A HREF="#DatabaseApplicationsActiveSites">identify putative active site residues</A></LI>
|
||
</UL>
|
||
</UL>
|
||
</UL>
|
||
|
||
<A NAME="TOCDatabaseFeatures"></A>
|
||
<UL>
|
||
<LI><A HREF="#DatabaseFeatures"><B>Useful Features</B> of the Molecular Modeling Database</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#FacilitateComputation"><B>Facilitate computation</B> on 3D structure data</A></LI>
|
||
<LI><A HREF="#ComputationalAnalyses"><B>Analysis</B> of individual structures and relationships among them</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#GeometricalFeatures"><B>biological and geometrical features</B> within 3D structures</A></LI>
|
||
<LI><A HREF="#ConservedDomainAnnotations"><B>conserved protein domain annotations</B></A></LI>
|
||
<LI><A HREF="#EvolutionaryRelationships"><B>evolutionary relationships</B> among 3D structures</A></LI>
|
||
<LI><A HREF="#FunctionalRelationships"><B>functional relationships</B> among 3D structures</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#SequenceStructureRelationship">Interactive views of <B>sequence-structure relationships</B></A></LI>
|
||
<LI><A HREF="#DataConnections"><B>Connections</B> between 3D structure records and associated literature, molecular, and chemical data</A></LI>
|
||
|
||
</UL>
|
||
</UL>
|
||
|
||
<UL>
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||
<LI><A HREF="#DatabaseContent"><B>Content</B> of the Molecular Modeling Database</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SourceDatabases"><B>Source database</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SourceDatabases"><!-- A HREF="http://www.rcsb.org/pdb/" -->RSCB Protein Data Bank (PDB)</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#DataProcessing">How are the <B>data processed</B> at NCBI?</A></LI>
|
||
|
||
<UL>
|
||
|
||
<!-- LI><A HREF="#DataProcessingASN1Format">conversion to ASN.1 format</A></LI -->
|
||
|
||
<LI><A HREF="#DataProcessingValidation">content <B>validation</B></A></LI>
|
||
|
||
<LI><A HREF="#DataProcessingDeposition">deposit <B>sequence and chemical data</B> into Entrez Protein, Nucleotide, and PubChem databases</A></LI>
|
||
|
||
<!-- LI><A HREF="#DataProcessingDataAnalysis">data analysis</A></LI -->
|
||
|
||
<LI><A HREF="#DataProcessingBiologicalForms">identify <B>biological units</B> (oligomeric states)</A> <I>(<A HREF="#DataProcessingHumanHemoglobinExamples"><span style="color:#d70000">illustrated example</span></A>)</I></LI>
|
||
<UL>
|
||
<!-- LI><A HREF="#DataProcessingBiologicalFormsOverview">What is a biological unit?</A></LI>
|
||
<LI><A HREF="#DataProcessingBiologicalFormsExamples">examples</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingHumanHemoglobinExamples">human hemoglobin</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingHumanHemoglobinExample1">human hemoglobin example 1 (complete biological unit)</A></LI>
|
||
<LI><A HREF="#DataProcessingHumanHemoglobinExample2">human hemoglobin example 2 (half of the biological unit)</A></LI>
|
||
<LI><A HREF="#DataProcessingHumanHemoglobinExample3">human hemoglobin example 3 (two copies of the biological unit)</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault">rat liver vault</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault_split1">rat liver vault split file 1 (2ZUO, MMDB ID 68966)</A></LI>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault_split2">rat liver vault split file 2 (2ZV4, MMDB ID 68967)</A></LI>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault_split3">rat liver vault split file 3 (2ZV5, MMDB ID 68968)</A></LI>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault_merged">rat liver vault merged file (MMDB ID 99596)</A></LI>
|
||
</UL>
|
||
</UL -->
|
||
<!-- LI><A HREF="#DataProcessingBiologicalFormsProcedures">procedures</A></LI>
|
||
<!-- UL -->
|
||
<LI><A HREF="#DataProcessingBiologicalFormsRemark350">author/software determination</A></LI>
|
||
<LI><A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">apply transformations derived from crytallographic symmetry</A></LI>
|
||
<LI><A HREF="#DataProcessingBiologicalFormsTypeClassification">compare biological units within a record to each other to identify distinct forms</A></LI>
|
||
<LI><A HREF="#DataProcessingBiologicalFormsMergeSplitFiles">note about biological units in merged PDB split files</A></LI>
|
||
<LI><A HREF="#DataProcessingAsymmetricUnit">technical note about asymmetric unit</A></LI>
|
||
<!-- /UL -->
|
||
<!-- LI><A HREF="#DataProcessingBiologicalFormsAdditionalNotes">additional notes</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingAsymmetricUnit">asymmetric unit (technical note)</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
|
||
<LI><A HREF="#DataProcessingMergeSplitFiles"><B>merge PDB split files</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_1VU0_ViralCapsidAav6"><span style="color:#d70000"><I>illustrated example</I></span>: viral capsid <!-- (adeno-associated virus serotype 6) --></A></LI>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault"><span style="color:#d70000"><I>illustrated example</I></span>: rat liver vault</A></LI>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel"><span style="color:#d70000"><I>illustrated example</I></span>: ribosome</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#DataProcessingInteractions">identify <B>interactions</B> among molecular components</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingInteractionsDistanceThreshold">4 Å interatomic distance</A><!-- Å is the HTML code for Angstrom, <20> --></LI>
|
||
<LI><A HREF="#DataProcessingInteractionsContactNumberThreshold">5 or more contacts</A></LI>
|
||
<LI><A HREF="#DataProcessingInteractionsRank">rank interactions</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#DataProcessingGeometricalFeatures">identify <B>geometrical features</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingSecondaryStructures">secondary structures in protein molecules</A></LI>
|
||
<LI><A HREF="#DataProcessing3dDomains">3D domains in protein molecules</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#DataProcessingGenes">identify the <B>gene</B> that corresponds to each protein</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingGeneSymbol">gene symbol</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#DataProcessingSimilarStructures">identify <B>relationships among 3D structures</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingSimilarStructuresVAST"><!-- VAST neighbors (similar 3D structures) -->find similar 3D structures using VAST algorithm </A></LI>
|
||
<!-- LI><A HREF="#DataProcessingSimilarStructuresIBIS">[IBIS clustering of similar structures by interaction types]cluster similar 3D structures by interaction type using IBIS</A></LI -->
|
||
</UL>
|
||
|
||
<!-- LI><A HREF="#DataProcessing______">______________________</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataProcessing______">______________________</A></LI>
|
||
<LI><A HREF="#DataProcessing______">______________________</A></LI>
|
||
<LI><A HREF="#DataProcessing______">{interactions among molecular components and oligomeric states}</A></LI>
|
||
</UL -->
|
||
|
||
<LI><A HREF="#DataProcessingCreateLinks">create <B>links to associated data</B> throughout the Entrez system</A></LI>
|
||
<!-- UL>
|
||
<LI><A HREF="#DataProcessingDirectLinks">create direct links to proteins, nucleotides, chemicals, literature, and taxonomy</A></LI>
|
||
<LI><A HREF="#DataProcessingIndirectLinks">calculate indirect links to additional data types</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
|
||
<LI><A HREF="#DataTypes"><B>Record types</B> <I>(<span style="color:#d70000">illustrated examples</span>)</I></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DataTypeExperimentalMethods">experimental methods (X-ray crystallography, NMR, other)</A></LI>
|
||
<LI><A HREF="#DataTypeMolecularComponents">molecule types (protein, DNA, RNA)</A></LI>
|
||
<!-- LI><A HREF="#DataTypeOther">other</A></LI -->
|
||
</UL>
|
||
<LI><A HREF="#DataProcessingUpdateFrequency"><B>Update frequency</B></A></LI>
|
||
</UL>
|
||
</UL>
|
||
|
||
|
||
<A NAME="TOCSearchTips"></A>
|
||
<UL>
|
||
<LI><A HREF="#SearchTips"><B>INPUT:  Search Tips</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SearchTipsInputValues"><B>Allowable search terms</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SearchByTextTerm">text terms (names of proteins, bound chemicals, authors, etc.)</A></LI>
|
||
<LI><A HREF="#SearchByUID">unique identifiers</A></LI>
|
||
<LI><A HREF="#SearchByOrganism">organism</A></LI>
|
||
<LI><A HREF="#SearchByDatabaseSubset">database subset</A></LI>
|
||
<LI><A HREF="#SearchByOther">and more...</A></LI>
|
||
</UL>
|
||
<LI><A NAME="TOCSearchMethods"></A><A HREF="#SearchMethods"><B>Search methods</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SearchMethodBasic">Basic search</A> (& <A HREF="#SearchDetails">search details</A>)</LI>
|
||
<LI><A HREF="#SearchMethodLimits">Limits</A></LI>
|
||
<LI><A HREF="#SearchMethodAdvanced">Advanced search</A> (<A HREF="#SearchBuilder">Search builder</A>, <A HREF="#SearchMethodShowIndex">Show index list</A>, <!--A HREF="#SearchMethodPreview">Preview</A --><A HREF="#SearchMethodHistory">History</A>)</LI>
|
||
<LI><A HREF="#SearchMethodComplexBoolean">Complex Boolean query</A></LI>
|
||
<LI><A HREF="#SearchMethodRangeQuery">Range search (range of dates, molecular weights, etc.)</A></LI>
|
||
</UL>
|
||
<LI><A NAME="TOCSearchFields"></A><A HREF="#SearchFields"><B>Search fields</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SearchFields">complete list of search field names, abbreviations, and descriptions</A></LI>
|
||
|
||
<!-- LI><A HREF="#SearchFieldAll">All Fields</A></LI>
|
||
<LI><A HREF="#SearchFieldAbstract">Abstract</A></LI>
|
||
<LI><A HREF="#SearchFieldAsuBiopolymerCount">ASU Biopolymer Count</A></LI>
|
||
<LI><A HREF="#SearchFieldAsuDNAMoleculeCount">ASU DNA Molecule Count</A></LI>
|
||
<LI><A HREF="#SearchFieldAsuChemicalCount">ASU Chemical Count</A></LI>
|
||
<LI><A HREF="#SearchFieldAsuOtherMoleculeCount">ASU Other Molecule Count</A></LI>
|
||
<LI><A HREF="#SearchFieldAsuProteinMoleculeCount">ASU Protein Molecule Count</A></LI>
|
||
<LI><A HREF="#SearchFieldAsuRNAMoleculeCount">ASU RNA Molecule Count</A></LI>
|
||
<LI><A HREF="#SearchFieldAuthor">Author</A></LI>
|
||
<LI><A HREF="#SearchFieldBiopolymerCount">BioUnit Biopolymer Count</A></LI>
|
||
<LI><A HREF="#SearchFieldDNAMoleculeCount">BioUnit DNA Molecule Count</A></LI>
|
||
<LI><A HREF="#SearchFieldLigCount">BioUnit Chemical Count</A></LI>
|
||
<LI><A HREF="#SearchFieldBioUnitMolecularWeight">BioUnit Molecular Weight</A></LI>
|
||
<LI><A HREF="#SearchFieldOtherMoleculeCount">BioUnit Other Molecule Count</A></LI>
|
||
<LI><A HREF="#SearchFieldProteinMoleculeCount">BioUnit Protein Molecule Count</A></LI>
|
||
<LI><A HREF="#SearchFieldRNAMoleculeCount">BioUnit RNA Molecule Count</A></LI>
|
||
[<LI><A HREF="#SearchFieldChemicalDescription">[<A HREF="#SearchFieldLigDescr">]Chemical Description</A></LI>]
|
||
<LI><A HREF="#SearchFieldChemicalName">[<A HREF="#SearchFieldLigName">]Chemical Name</A></LI>
|
||
<LI><A HREF="#SearchFieldChemicalSynonyms">Chemical Synonyms</A></LI>
|
||
<LI><A HREF="#SearchFieldConservedDomainDatabaseDescription">Conserved Domain Database Description</A></LI>
|
||
<LI><A HREF="#SearchFieldConservedDomainDescription">Conserved Domain Description</A></LI>
|
||
<LI><A HREF="#SearchFieldConservedDomainPSSMID">Conserved Domain PSSMID</A></LI>
|
||
<LI><A HREF="#SearchFieldConservedDomainShortName">Conserved Domain Short Name</A></LI>
|
||
<LI><A HREF="#SearchFieldConservedDomainTitle">Conserved Domain Title</A></LI>
|
||
<LI><A HREF="#SearchFieldConservedDomainSuperfamilyDescription">Conserved Domain Superfamily Description</A></LI>
|
||
<LI><A HREF="#SearchFieldConservedDomainSuperfamilyPSSMID">Conserved Domain Superfamily PSSMID</A></LI>
|
||
<LI><A HREF="#SearchFieldConservedDomainSuperfamilyShortName">Conserved Domain Superfamily Short Name</A></LI>
|
||
<LI><A HREF="#SearchFieldConservedDomainSuperfamilyTitle">Conserved Domain Superfamily Title</A></LI>
|
||
<LI><A HREF="#SearchFieldDNAName">DNA Name</A></LI>
|
||
<LI><A HREF="#SearchFieldECRNnumber">EC/RN Number</A></LI>
|
||
<LI><A HREF="#SearchFieldExperimentalMethod">[<A HREF="#SearchFieldExpMethod"</A>]Experimental Method</A></LI>
|
||
<LI><A HREF="#SearchFieldGeneDescription">Gene Description</A></LI>
|
||
<LI><A HREF="#SearchFieldGeneName">Gene Name</A></LI>
|
||
<LI><A HREF="#SearchFieldFilter">Filter</A></LI>
|
||
<LI><A HREF="#SearchFieldJournal">Journal</A></LI>
|
||
<LI><A HREF="#SearchFieldMMDBEntryDate">MMDB Entry Date</A></LI>
|
||
<LI><A HREF="#SearchFieldMMDBID">[<A HREF="#SearchFieldUID">]MMDB ID</A></LI>
|
||
<LI><A HREF="#SearchFieldMMDBModifyDate">MMDB Modify Date</A></LI>
|
||
<LI><A HREF="#SearchFieldNumberOfPDBRecordsPerStructure">Number of PDB Records per Structure</A></LI>
|
||
[<LI><A HREF="#SearchFieldModDNAResCount">ModDNAResCount</A> |
|
||
<A HREF="#SearchFieldModProteinResCount">ModProteinResCount</A> |
|
||
<A HREF="#SearchFieldModRNAResCount">ModRNAResCount</A> | </LI>]
|
||
<LI><A HREF="#SearchFieldOligomericState">Oligomeric State</A></LI>
|
||
<LI><A HREF="#SearchFieldOrganism">Organism</A></LI>
|
||
<LI><A HREF="#SearchFieldOtherMoleculeName">Other Molecule Name</A></LI>
|
||
<LI><A HREF="#SearchFieldPdbAccession">[<A HREF="#SearchFieldPdbAcc">]PDB Accession</A> </LI>
|
||
<LI><A HREF="#SearchFieldPDBChemicalCode">[<A HREF="#SearchFieldLigCode">]PDB Chemical Code</A></LI>
|
||
[<LI><A HREF="#SearchFieldPdbChainCode">PDB Chain Code</A></LI>]
|
||
<LI><A HREF="#SearchFieldPdbClass">PDB Class</A></LI>
|
||
<LI><A HREF="#SearchFieldPdbComment">PDB Comment</A></LI>
|
||
<LI><A HREF="#SearchFieldPDBDepositDate">PDB Deposit Date</A></LI>
|
||
<LI><A HREF="#SearchFieldPdbDescription">[<A HREF="SearchFieldPdbDescr">]PDB Description</A></LI>
|
||
<LI><A HREF="#SearchFieldPdbFileCount">PDB File Count</A></LI>
|
||
<LI><A HREF="#SearchFieldPdbSource">PDB Source</A></LI>
|
||
<LI><A HREF="#SearchFieldProteinName">Protein Name</A></LI>
|
||
<LI><A HREF="#SearchFieldResolution">Resolution</A></LI>
|
||
<LI><A HREF="#SearchFieldRNAName">RNA Name</A></LI>
|
||
<LI><A HREF="#SearchFieldTitle">Title</A>
|
||
<!-- LI><A HREF="#______">__________</A> |
|
||
<A HREF="#______">__________</A> |
|
||
<A HREF="#______">__________</A> | </LI -->
|
||
|
||
<LI><A HREF="#SearchFieldTips">tips about search field abbreviations</A>, <A HREF="#SearchTipsQuotes">use of quotes around query terms</A>, and <A HREF="#SearchTipsTruncation">use of wild-card (*)</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#LinkFromOtherDatabase"><B>Link from other Entrez database</B></A> <I>(<A HREF="#LinkFromOtherDatabaseIllustration"><span style="color:#d70000">illustrated example</span></A>)</I></LI>
|
||
<UL>
|
||
<LI><A HREF="#LinkFromOtherDatabase">traverse from sequence/literature/small molecule/other databases to 3D structures</A></LI>
|
||
<LI><A HREF="#LinksFromProteinToStructure">links from protein sequence records to 3D structures</A></LI>
|
||
</UL>
|
||
</UL>
|
||
</UL>
|
||
|
||
|
||
<A NAME="TOCSearchResults"></A>
|
||
<UL>
|
||
<LI><A HREF="#SearchResults"><B>OUTPUT:  Search Results</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DocSumPage"><B>Document summary (docsum) page</B>: list of records found <I>(<span style="color:#d70000">illustrated example</span>)</I></A><!-- and <A HREF="#DocSumDisplayOptions"></A> --></LI>
|
||
<UL>
|
||
<LI><A HREF="#DocSumDisplayMenu">"Display Settings" menu</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DocSumFormat">Format</A></LI>
|
||
<LI><A HREF="#DocSumShow">Items per page</A></LI>
|
||
<LI><A HREF="#DocSumSort">Sort By</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#DocSumSendTo">"Send To" menu</A></LI>
|
||
<LI><A HREF="#Filters">Filter your results</A></LI>
|
||
<LI><A HREF="#SelectedRecords">Refine your results</A></LI>
|
||
<!-- UL>
|
||
<LI><A HREF="#SelectedRecordsProteinDomainFamilies">Protein Domain Families</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SelectedRecordsProteinDomainSpecificHits">Families</A></LI>
|
||
<LI><A HREF="#SelectedRecordsProteinDomainSuperfamilies">Superfamilies</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#SelectedRecordsComplexes">Complexes</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SelectedRecordsComplexesProteinProtein">Protein-Protein</A></LI>
|
||
<LI><A HREF="#SelectedRecordsComplexesProteinDNA">Protein-DNA</A></LI>
|
||
<LI><A HREF="#SelectedRecordsComplexesProteinRNA">Protein-RNA</A></LI>
|
||
<LI><A HREF="#SelectedRecordsComplexesProteinChemical">Protein-Chemical</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#SelectedRecordsLiterature">Literature</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SelectedRecordsPubMed">PubMed</A></LI>
|
||
<LI><A HREF="#SelectedRecordsPMC">PMC</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#SelectedRecordsTaxonomy">Taxonomy</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
<LI><A NAME="TOCDocSumLinks"></A><A HREF="#DocSumLinks"><B>Find related data</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#LinksSimilarStructures"><!-- A HREF="#LinksRelatedStructures" -->Similar Structures</A></LI>
|
||
<LI><A HREF="#LinksLiterature">Literature</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#LinksPMC">PubMed Central Full Text</A></LI>
|
||
<LI><A HREF="#LinksPubMed">PubMed Citations</A></LI>
|
||
<!-- LI><A HREF="#LinksOMIM">[OMIM]</A></LI -->
|
||
</UL>
|
||
<LI><A HREF="#LinksDomains">Domains</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#LinksConservedDomainFamily">Conserved Domain Family</A></LI>
|
||
<LI><A HREF="#LinksConservedDomainSuperfamily">Conserved Domain Superamily</A></LI>
|
||
<LI><A HREF="#LinksConservedDomains">Conserved Domains</A></LI>
|
||
<!-- LI><A HREF="#Links3dDomains">3D Domains</A></LI -->
|
||
</UL>
|
||
<LI><A HREF="#LinksChemicals">Chemicals</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#LinksPubChemCompound">PubChem Compound</A></LI>
|
||
<LI><A HREF="#LinksPubChemSubstance">PubChem Substance</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#LinksSequences">Sequences</A></LI>
|
||
<UL>
|
||
<!-- LI><A HREF="#LinksGenome">Genome</A></LI -->
|
||
<LI><A HREF="#LinksGene">Gene</A></LI>
|
||
<LI><A HREF="#LinksNucleotide">Nucleotide</A></LI>
|
||
<!-- LI><A HREF="#LinksEST">EST</A></LI -->
|
||
<!-- LI><A HREF="#LinksGSS">GSS</A></LI -->
|
||
<!-- LI><A HREF="#LinksSNP">SNP</A></LI -->
|
||
<LI><A HREF="#LinksProtein">Protein</A></LI>
|
||
<LI><A HREF="#LinksProteinRelated">Related Protein</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#LinksOther">Other Links</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#LinksBioAssay">BioAssay</A></LI>
|
||
<LI><A HREF="#LinksBioSystem">BioSystem</A></LI>
|
||
<!-- LI><A HREF="#LinksGenome">Genome</A></LI -->
|
||
<!-- LI><A HREF="#LinksEST">EST</A></LI -->
|
||
<!-- LI><A HREF="#LinksGSS">GSS</A></LI -->
|
||
<!-- LI><A HREF="#LinksNucleotide">Nucleotide</A></LI -->
|
||
<LI><A HREF="#LinksOMIM">OMIM</A></LI>
|
||
<!-- LI><A HREF="#LinksProtein">Protein</A></LI -->
|
||
<!-- LI><A HREF="#LinksProteinRelated">Related Proteins</A></LI -->
|
||
<!-- LI><A HREF="#LinksSNP">SNP</A></LI -->
|
||
<LI><A HREF="#LinksTaxonomy">Taxonomy</A></LI>
|
||
</UL>
|
||
</UL>
|
||
<LI><A HREF="#ViewIndividualRecord"><B>View details</B> for an individual 3D structure record</A></LI>
|
||
</UL>
|
||
</UL>
|
||
|
||
<A NAME="TOCSummaryPage"></A>
|
||
<UL>
|
||
<LI><A HREF="#SummaryPage"><B>Structure Summary Page</B>:  What information is displayed for each macromolecular structure? <I>(<span style="color:#d70000">illustrated example</span>)</I></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvRecordIdentifiers"><B>Record identifiers</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvPDBID">PDB ID</A></LI>
|
||
<LI><A HREF="#MmdbsrvMMDBID">MMDB ID</A></LI>
|
||
<!-- LI><A HREF="#MmdbsrvSearchButton">Search Button</A></LI -->
|
||
</UL>
|
||
|
||
<LI><A HREF="#MmdbsrvDescriptiveInfo"><B>Descriptive information</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvDescription">Title</A></LI>
|
||
<LI><A HREF="#MmdbsrvReference">Citation<!-- Reference --></A></LI>
|
||
<LI><A HREF="#MmdbsrvDeposited">PDB deposit date</A></LI>
|
||
<LI><A HREF="#MmdbsrvUpdatedInMMDB">MMDB update date</A></LI>
|
||
<!-- UL>
|
||
<LI><A HREF="#MmdbsrvMMDBVersion">MMDB version</A></LI>
|
||
</UL -->
|
||
<LI><A HREF="#MmdbsrvTaxonomy">Source organism</A></LI>
|
||
<LI><A HREF="#MmdbsrvSimilarStructures"><!-- A HREF="#LinksSimilarStructures" --><!-- A HREF="#LinksRelatedStructures" -->Similar structures: VAST+</A></LI>
|
||
<!-- LI><A HREF="#MmdbsrvInferredInteractions">Inferred interactions: IBIS</A></LI -->
|
||
<LI><A HREF="#MmdbsrvExperimentalMethod">Experimental method</A></LI>
|
||
<LI><A HREF="#MmdbsrvResolution">Resolution</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#MmdbsrvDisplayOptions"><B>Display options</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvDisplayOptionsConcise">Default biological unit</A></LI>
|
||
<LI><A HREF="#MmdbsrvDisplayOptionsComplete">All biologicial units</A></LI>
|
||
<LI><A HREF="#MmdbsrvDisplayOptionsAsymmetric">Asymmetric unit</A></LI>
|
||
</UL>
|
||
|
||
<LI><!-- A HREF="#MmdbsrvThumbnailImages" --><A HREF="#MmdbsrvStructureImages"><B>Structure images</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvThumbnailMolecularGraphic">Molecular graphic</A></LI>
|
||
<!-- UL>
|
||
<LI><A HREF="#MmdbsrvThumbnailMolecularGraphicBiologicalForm">Biological Unit</A></LI>
|
||
<LI><A HREF="#MmdbsrvThumbnailMolecularGraphicAsymmetricUnit">Asymmetric Unit</A></LI>
|
||
</UL -->
|
||
<LI><A HREF="#MmdbsrvThumbnailSchematic">Interactions schematic</A></LI>
|
||
<!-- UL>
|
||
<LI><A HREF="#MmdbsrvThumbnailSchematicMolecularComponents">Molecular Components</A></LI>
|
||
<LI><A HREF="#MmdbsrvThumbnailSchematicInteractions">Interactions</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
|
||
<LI><A HREF="#MmdbsrvStructureView"><B>Download structure data (save 3D structure record)</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormat"><!-- A HREF="#MmdbsrvStructureViewProgram" -->Format</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormatCn3D"><!-- A HREF="#MmdbsrvStructureViewInCn3D" -->ASN.1 (Cn3D)</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormatPDB"><!-- A HREF="#MmdbsrvStructureViewInRasmol" -->PDB</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormatXML">XML</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormatJSON">JSON</A></LI>
|
||
<!-- LI><A HREF="#MmdbsrvStructureViewInJMol">JMol</A></LI -->
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormatPNG">PNG (image)</A></LI>
|
||
</UL>
|
||
<!-- LI><A HREF="#MmdbsrvStructureViewDisplayAs">Display As</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureView3DStructure">3D Structure</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewSeeFile">See File</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewSaveFile">Save File</A></LI>
|
||
</UL -->
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSet">Data Set</A>
|
||
<!-- A HREF="#MmdbsrvStructureViewDrawing">Drawing</A><A HREF="#MmdbsrvStructureViewComplexity">Complexity</A --></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSetAllAtoms"><!-- A HREF="#MmdbsrvStructureViewDrawingAllAtoms" --><!-- A HREF="#MmdbsrvStructureViewComplexityAllAtoms" -->Single 3D structure</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSetAllModels"><!-- A HREF="#MmdbsrvStructureViewDrawingAllModels" --><!-- A HREF="#MmdbsrvStructureViewComplexityAllModels" -->All 3D structures</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSetBackbone"><!-- A HREF="#MmdbsrvStructureViewDrawingBackbone" --><!-- A HREF="#MmdbsrvStructureViewComplexityBackbone" -->Alpha carbons</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSetPDBdataset">PDB source file</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#MmdbsrvSave">Additional details about structure data download options</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#DownloadStructureDataIllustration"><span style="color:#d70000"><I>annotated illustration</I></span> of download options</A></LI>
|
||
<LI><A HREF="#MmdbsrvSaveDataFile">details about data saved in each file format</A><!-- BR><A HREF="#MmdbsrvSaveASN1format">ASN.1 (Cn3D)</A>, <A HREF="#MmdbsrvSavePDBformat">PDB</A>, <A HREF="#MmdbsrvSaveXMLformat">XML and JSON</A --></LI>
|
||
<LI><A HREF="#MmdbsrvSave3dView">save image of 3D structure</A></LI>
|
||
<LI><A HREF="#MmdbsrvSaveComponents">save structure components</A></LI>
|
||
</UL>
|
||
|
||
<!-- LI><A HREF="#MmdbsrvStructureViewURLformat">Web API:  URL format for displaying or saving a structure record</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#StructureViewURLformatBaseURL">base URL</A></LI>
|
||
<LI><A HREF="#StructureViewURLformatParameters">parameters & allowable values</A></LI>
|
||
<LI><A HREF="#StructureViewURLformatExamples">examples of URLs for displaying or saving 3D structure records</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
<LI><A NAME="TOCMmdbsrvMolecularComponents"></A><A HREF="#MmdbsrvMolecularComponents"><B>Molecular components</B></A><!-- A HREF="#MmdbsrvMolecularComponentsInteractions">interactions</A> & <A HREF="#MmdbsrvMolecularComponentsAnnotations">feature annotations</A --></LI>
|
||
<UL>
|
||
<LI><A HREF="#MolecularComponentsTable"><!-- A HREF="#MmdbsrvMolecularComponentsTable" -->Tabular list of molecular components</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvColumnHeaders">Column headers: label, count, molecule</A></LI>
|
||
<!-- UL>
|
||
<LI><A HREF="#MmdbsrvColumnHeadersLabel">Label</A></LI>
|
||
<LI><A HREF="#MmdbsrvColumnHeadersCount">Count</A></LI>
|
||
<LI><A HREF="#MmdbsrvColumnHeadersMolecule">Molecule</A></LI>
|
||
<LI><A HREF="#MmdbsrvColumnHeadersInteractions">Interactions</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
<LI><A HREF="#MmdbsrvProteins">Proteins</A></LI>
|
||
<UL>
|
||
<LI>
|
||
<A HREF="#MmdbsrvProteins">Molecule label, count, & name</A>
|
||
<!-- A HREF="#MmdbsrvProteinsMoleculeLabel">label</A -->
|
||
<!-- A HREF="#MmdbsrvProteinsMoleculeCount">count</A -->
|
||
<!-- A HREF="#MmdbsrvProteinsMoleculeName">name</A -->
|
||
<!-- A HREF="#MmdbsrvProteinsMoleculeInteractions">interactions</A -->
|
||
</LI>
|
||
<LI><A HREF="#MmdbsrvProteinsGeneSymbol">Gene symbol</A></LI>
|
||
<LI><A HREF="#MmdbsrvProteinsShowAnnotation">Protein annotation graphic</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvProteins3dDomains">3D domains</A></LI>
|
||
<LI><A HREF="#MmdbsrvProteinsClassification">Domain families (protein classification)</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvProteinsClassificationSpecificHits">Specific hits</A></LI>
|
||
<LI><A HREF="#MmdbsrvProteinsClassificationSuperfamilies">Superfamilies</A></LI>
|
||
<LI><A HREF="#MmdbsrvProteinsClassificationMultidomains">Multidomains</A></LI>
|
||
</UL>
|
||
<!-- LI><A HREF="#MmdbsrvProteinsSimilarSequences">Similar Sequences (BLAST)</A></LI -->
|
||
<!-- LI><A HREF="#MmdbsrvProteinsSimilarStructures">Similar 3D Structures: VAST</A></LI -->
|
||
</UL>
|
||
<!-- LI><A HREF="#MmdbsrvProteinsMoleculeInteractions">Interactions</A></LI -->
|
||
</UL>
|
||
<LI><A HREF="#MmdbsrvNucleotides">Nucleotides</A></LI>
|
||
<UL>
|
||
<LI>
|
||
<A HREF="#MmdbsrvNucleotidesMoleculeName">Molecule label, count, & name</A>
|
||
<!-- A HREF="#MmdbsrvNucleotidesMoleculeLabel">label</A -->
|
||
<!-- A HREF="#MmdbsrvNucleotidesMoleculeCount">count</A -->
|
||
<!-- A HREF="#MmdbsrvNucleotidesMoleculeName">name</A -->
|
||
<!-- A HREF="#MmdbsrvNucleotidesMoleculeInteractions">interactions</A -->
|
||
</LI>
|
||
<LI><A HREF="#MmdbsrvNucleotidesThumbnail">Thumbnail graphic</A></LI>
|
||
<!-- LI><A HREF="#MmdbsrvNucleotidesMoleculeInteractions">Interactions</A></LI -->
|
||
</UL>
|
||
<LI><A HREF="#MmdbsrvChemicals">Chemicals</A></LI>
|
||
<UL>
|
||
<LI>
|
||
<A HREF="#MmdbsrvChemicalsMoleculeName">Molecule label, count, & name</A>
|
||
<!-- A HREF="#MmdbsrvChemicalsMoleculeLabel">label</A -->
|
||
<!-- A HREF="#MmdbsrvChemicalsMoleculeCount">count</A -->
|
||
<!-- A HREF="#MmdbsrvChemicalsMoleculeName">name</A -->
|
||
<!-- A HREF="#MmdbsrvChemicalsMoleculeInteractions">interactions</A -->
|
||
</LI>
|
||
<LI><A HREF="#MmdbsrvChemicalsThumbnail">Thumbnail graphic</A></LI>
|
||
<!-- LI><A HREF="#MmdbsrvChemicalsMoleculeInteractions">Interactions</A></LI -->
|
||
</UL>
|
||
<LI><A HREF="#MmdbsrvNonStandardBiopolymers">Non-standard Biopolymers</A></LI>
|
||
<UL>
|
||
<LI>
|
||
<A HREF="#MmdbsrvNonStandardBiopolymersMoleculeName">Molecule label, count, & name</A>
|
||
<!-- A HREF="#MmdbsrvNonStandardBiopolymersMoleculeLabel">label</A -->
|
||
<!-- A HREF="#MmdbsrvNonStandardBiopolymersMoleculeCount">count</A -->
|
||
<!-- A HREF="#MmdbsrvNonStandardBiopolymersMoleculeName">name</A -->
|
||
<!-- A HREF="#MmdbsrvNonStandardBiopolymersMoleculeInteractions">interactions</A -->
|
||
</LI>
|
||
<!-- LI><A HREF="#MmdbsrvNonStandardBiopolymersThumbnail">Thumbnail graphic</A></LI -->
|
||
<!-- LI><A HREF="#MmdbsrvNonStandardBiopolymersMoleculeInteractions">Interactions</A></LI -->
|
||
</UL>
|
||
<!-- LI><A HREF="#MmdbsrvInteractions">Observed [Inferred?] Interactions</A></LI -->
|
||
<!-- UL>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
<!-- LI><A HREF="#MmdbsrvSave"><B>Save</B> structure record <I>(<span style="color:#d70000">illustrated example</span>)</I></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvSaveASN1format"><B>ASN.1 format</B></A></LI>
|
||
<LI><A HREF="#MmdbsrvSavePDBformat"><B>PDB format</B></A></LI>
|
||
</UL -->
|
||
</UL>
|
||
</UL>
|
||
|
||
|
||
<A NAME="TOCWebAPI"></A>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureViewURLformat"><B>Web API</B>:  URL format for displaying or saving a structure record</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#StructureViewURLformatBaseURL">base URL</A></LI>
|
||
<LI><A HREF="#StructureViewURLformatParameters">parameters & allowable values</A></LI>
|
||
<LI><A HREF="#StructureViewURLformatExamples">examples of URLs for displaying or saving 3D structure records</A></LI>
|
||
</UL>
|
||
</UL>
|
||
|
||
<A NAME="TOCReferences"></A>
|
||
<UL>
|
||
<LI><A HREF="#References"><B>References</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#Citing">Citing the Molecular Modeling Database</A></LI>
|
||
<LI><A HREF="#ReferencesAdditional">Additional references</A></LI>
|
||
<!--LI><A HREF="#CitingBiosystemsRecord">Citing an individual macromolecular structure record</A></LI-->
|
||
<!-- LI><A HREF="#ReferencesSourceDatabases">Article describing the source database</A></LI -->
|
||
</UL>
|
||
</UL>
|
||
|
||
</TD>
|
||
|
||
<!-- ======= SPACER_COLUMN_TO_RIGHT_OF_TOC_LEFT_SIDE_TEXT ========= -->
|
||
|
||
<TD class="WhiteCell TOCText" width="5"> </TD>
|
||
|
||
|
||
<!-- =============== RIGHT_SIDE_THUMBNAILS ================ -->
|
||
|
||
<TD WIDTH="300" class="WhiteCell ThumbText" ALIGN="LEFT" VALIGN="TOP">
|
||
|
||
<!-- BR -->
|
||
|
||
<!-- =============== BRIEF_TABLE_OF_CONTENTS ================ -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
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<TR>
|
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<TABLE width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
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<TR>
|
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<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;">BRIEF TABLE OF CONTENTS</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE width="100%" border="0" class="Yellow1CellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<TR>
|
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<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP" colspan="3"> </TD>
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</TR>
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<TR>
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<TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
<TD ALIGN="Left" VALIGN="TOP" style="white-space: nowrap;" class="Yellow1Cell">
|
||
|
||
<A HREF="#WhatIs">What are macromolecular structures?</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#DatabaseApplications">How can they be used?</A><BR>
|
||
|
||
<A HREF="#DatabaseFeatures">Useful features of database</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#FacilitateComputation">Computation</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#ComputationalAnalyses">Analysis</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SequenceStructureRelationship">Sequence-structure relationships</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#DataConnections">Connections to associated data</A><BR>
|
||
|
||
<A HREF="#DatabaseContent">Database content</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SourceDatabases">Source database</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#DataProcessing">Data processing</A> (<A HREF="#DataProcessingBiologicalForms">biounits</A>, <A HREF="#DataProcessingInteractions">interactions</A>,<BR><img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#DataProcessingMergeSplitFiles">merged PDB split files</A>)<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#DataTypes">Record types (X-ray/NMR, other)</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#DataProcessingUpdateFrequency">Update frequency</A><BR>
|
||
|
||
<A HREF="#SearchTips">Input:  Search tips</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SearchMethods">Search methods</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SearchFields">Search fields</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#LinkFromOtherDatabase">Link from other Entrez Database</A><BR>
|
||
|
||
<A HREF="#SearchResults">Output:  Search results</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#DocSumDisplayMenu">Display settings</A>, <A HREF="#DocSumSendTo">Send To</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#Filters">Filter your results</A><BR>
|
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<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SelectedRecords">Refine your results</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#DocSumLinks">Find related data</A><BR>
|
||
|
||
<A HREF="#SummaryPage">Structure Summary Page</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#MmdbsrvRecordIdentifiers">Identifiers (PDB ID, MMDB ID)</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#MmdbsrvDescriptiveInfo">Descriptive information</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><!-- A HREF="#LinksSimilarStructures" --><!-- A HREF="#LinksRelatedStructures" --><A HREF="#MmdbsrvSimilarStructures">Similar structures: VAST+</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#MmdbsrvInferredInteractions">Inferred interactions: IBIS</A><BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#MmdbsrvDisplayOptions">Display options (biological/asymmetrical)</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#MmdbsrvBiologicalUnit">Biological unit <I>N</I></A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><!-- A HREF="#MmdbsrvThumbnailImages" --><A HREF="#MmdbsrvStructureImages">Structure images</A> (<A HREF="#MolecularGraphic">molecular graphic</A>, <BR><img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#InteractionsSchematic">interactions schematic</A>)<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#MmdbsrvStructureView">Download Structure Data (save structure)</A><!-- (<A HREF="#MmdbsrvSave">illustration</A>) --><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#MmdbsrvMolecularComponents"><!-- A HREF="#MmdbsrvGraphicSummary" -->Molecular components</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#MmdbsrvAnnotations">Biological features</A><BR -->
|
||
|
||
<A HREF="#MmdbsrvStructureViewURLformat">Web API</A><BR>
|
||
|
||
<A HREF="#References">References</A><BR>
|
||
<!-- A HREF="#___">_________</A><BR -->
|
||
</TD>
|
||
<TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP" colspan="3"> </TD>
|
||
</TR>
|
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|
||
</TABLE>
|
||
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR>
|
||
<BR>
|
||
|
||
<!-- =============== END_BRIEF_TABLE_OF_CONTENTS ================ -->
|
||
|
||
|
||
<!-- SINGLE_THUMBNAIL_YELLOW_BACKGROUND_WHAT_ARE_MACROMOLECULAR_STRUCTURES -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
|
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|
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<TABLE width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
||
<TR>
|
||
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#WhatIs">WHAT ARE MACROMOLECULAR STRUCTURES?</A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE width="100%" border="0" class="Yellow1CellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<!-- TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD -->
|
||
<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="Yellow1Cell">
|
||
<A HREF="#WhatIs"><IMG src="images/1tup_p53_tumor_suppressor_thumbnail.png" width="280" height="280" border=0 align="center" alt="Thumbnail image showing 3D structure of Tumor Suppressor P53 Complexed with DNA (accession 1TUP). Yellow spheres represent amino acids within 5 Angstroms of DNA strands. Click on image to read about macromolecular structures and how they can be used to learn more about proteins and other biomolecules."></A>
|
||
</TD>
|
||
<!-- TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD -->
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR><BR>
|
||
|
||
|
||
<!-- == SINGLE_THUMBNAIL_YELLOW_BACKGROUND_SEQUENCE_STRUCTURE_RELATIONSHIP == -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
|
||
|
||
<TABLE width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
||
<TR>
|
||
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#DatabaseApplications">SEQUENCE-STRUCTURE-FUNCTION<BR>Example: structural basis of aspirin activity</A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE width="100%" border="0" class="Yellow1CellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<!-- TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD -->
|
||
<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="Yellow1Cell">
|
||
<A HREF="#DatabaseApplications"><IMG src="images/1PTH_thumbnail_help.png" width="280" height="420" border=0 align="center" alt="Thumbnail image of Prostaglandin H2 Synthase from sheep (accession 1PTH), showing 3D structure of active site and corresponding protein sequence data. Click on image to read more about interactive displays of sequence-structure relationships and how can 3D structures be used to learn more about proteins and other biomolecules."></A>
|
||
</TD>
|
||
<!-- TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD -->
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR><BR>
|
||
|
||
<!-- ======= SINGLE_THUMBNAIL_YELLOW_BACKGROUND_STRUCTURE_RECORD ======== -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
|
||
|
||
<TABLE width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
||
<TR>
|
||
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#SummaryPage">STRUCTURE SUMMARY PAGE (sample)</A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE width="100%" border="0" class="WhiteCellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<!-- TD ALIGN="Left" class="MiniText WhiteCell" VALIGN="TOP"> </TD -->
|
||
<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="WhiteCell">
|
||
<A HREF="#SummaryPage"><IMG src="images/1PTH_structure_summary_thumbnail_biounits.png" width="280" height="550" border=0 align="center" alt="Thumbnail image of a sample structure summary page, for sheep prostaglandin H2 synthase (MMDB ID 50885, PDB ID 1PTH). Click on the image to read more about the features and options on a structure summary page."></A>
|
||
</TD>
|
||
<!-- TD ALIGN="Left" class="MiniText WhiteCell" VALIGN="TOP"> </TD -->
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR><BR>
|
||
|
||
|
||
<!-- SINGLE_THUMBNAIL_YELLOW_BACKGROUND_MOLECULAR_GRAPHIC -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
|
||
|
||
<TABLE width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
||
<TR>
|
||
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#MmdbsrvThumbnailMolecularGraphic">MOLECULAR GRAPHIC
|
||
(static → interactive)</A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE width="100%" border="0" class="Yellow1CellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<!-- TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD -->
|
||
<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="WhiteCell">
|
||
<A HREF="#MmdbsrvThumbnailMolecularGraphic"><IMG SRC="images/1PTH_thumbnail_molecular_graphic_from_mmdbsrv_page.png" WIDTH="150" HEIGHT="750" BORDER="0" ALT="Sample thumbnail molecular graphic for 1PTH, prostaglandin H2 synthase-1 from sheep. A static image is shown by default. Click the 3D view button or the full-featured 3D viewer button near the bottom of a static molecular graphic to load an interactive view."></A>
|
||
</TD>
|
||
<!-- TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD -->
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR><BR>
|
||
|
||
<!-- SINGLE_THUMBNAIL_YELLOW_BACKGROUND_INTERACTIONS_SCHEMATIC -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
|
||
|
||
<TABLE width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
||
<TR>
|
||
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#MmdbsrvThumbnailInteractionsSchematic">INTERACTIONS SCHEMATIC</A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE width="100%" border="0" class="Yellow1CellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<!-- TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD -->
|
||
<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="WhiteCell">
|
||
<A HREF="#MmdbsrvThumbnailInteractionsSchematic"><IMG SRC="images/1PTH_interactions_schematic.png" WIDTH="150" HEIGHT="150" BORDER="1" ALT="Sample interactions schematic for sheep prostaglandin H2 sythase, from the 1PTH structure record."></A>
|
||
</TD>
|
||
<!-- TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD -->
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR><BR>
|
||
|
||
<!-- =========== ADDITIONAL_THUMBNAILS_WHITE_BACKGROUND ============== -->
|
||
|
||
<!-- BR><BR>
|
||
<A HREF="#______">Thumbnail header/key concept</A><br>
|
||
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
||
|
||
|
||
<BR><BR><BR>
|
||
<A HREF="#______">Thumbnail header/key concept</A><br>
|
||
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
||
|
||
|
||
<BR><BR><BR>
|
||
<A HREF="#______">Thumbnail header/key concept</A><br>
|
||
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
||
|
||
|
||
<BR><BR><BR>
|
||
<A HREF="#______">Thumbnail header/key concept</A><br>
|
||
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
||
|
||
<BR><BR -->
|
||
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- =========== PAGE_MARGIN_TO_RIGHT_OF_TABLE_OF_CONTENTS =============== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############ END_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT_AND_TOC ######## -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell MicroText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ######## BLUE_HEADER_SECTION_1_WHAT_ARE_MACROMOLECULAR_STRUCTURES ######### -->
|
||
|
||
<A NAME="WhatIs"></A>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1">What are macromolecular structures?</SPAN></TD>
|
||
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ###### END_BLUE_HEADER_SECTION_1_WHAT_ARE_MACROMOLECULAR_STRUCTURES ###### -->
|
||
|
||
|
||
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ########### -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
||
<TR>
|
||
<TD class="WhiteCellBlueEdgeAll">
|
||
|
||
<!-- ================= LEVEL_1 ==================== -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" class="NormalText" border="0" cellspacing="0" cellpadding="0">
|
||
|
||
<!-- ========= STRUCTURE_DETERMINES_FUNCTION_P53_EXAMPLE ======== -->
|
||
|
||
<TR>
|
||
<TD class="NormalText" ALIGN="LEFT" VALIGN="TOP">
|
||
|
||
<A NAME="StructureFunction"></A>
|
||
<BR>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<!-- ===== IMAGE_TO_RIGHT_OF_TEXT_P53_TUMOR_SUPPRESSOR_1TUP ===== -->
|
||
<A HREF="mmdb_how_to_view_in_cn3d.html#Illustration"><IMG src="images/1tup_p53_tumor_suppressor.png" width="400" height="440" border="0" align="right" alt="Image showing 3D structure of Tumor Suppressor P53 Complexed with DNA (accession 1TUP). Yellow spheres represent amino acids within 5 Angstroms of DNA strands. Click on the image for more information on how to generate this view using Cn3D."></A>
|
||
|
||
<!-- ===== END_IMAGE_TO_RIGHT_OF_TEXT_P53_TUMOR_SUPPRESSOR_1TUP ===== -->
|
||
|
||
<B>Macromolecular structures</B> show the three-dimensional shape of proteins and other biomolecules and provide a wealth of information on the <A HREF="#DatabaseApplications"><B>biological function</B>, on <B>mechanisms</B> linked to the function</A>, and on the evolutionary history of and <A HREF="#ComputationalAnalyses"><B>relationships</B></A> between macromolecules. Most structure data are obtained from <A HREF="#DataTypeExperimentalMethods">experimental methods</A> such as X-ray crystallography and NMR-spectroscopy.<BR><BR>
|
||
|
||
While <!-- A HREF="/sites/entrez?db=genome" -->genome projects and individual labs have deciphered the nucleotide sequences of genes and the linear protein sequences of their gene products, the functions of proteins and other biomolecules ultimately depend upon their shape. Because of this, the study of <A HREF="../../index.shtml">structural biology</A> is an important complement to genomics. Together, those fields contribute insights into the biology of thousands of organisms and provide a foundation for yet more research on <A HREF="../../cdd/cdd.shtml"><!-- A HREF="../../index.shtml#ConservedDomains" -->protein functions and classifications</A>, the <A HREF="https://pubchem.ncbi.nlm.nih.gov/"><!-- A HREF="../../index.shtml#SmallMolecules" -->chemicals</A> to which they bind, <A HREF="../../biosystems/docs/biosystems_about.html"><!-- A HREF="../../index.shtml#BioSystems" -->biological systems</A>, and more.
|
||
<BR><BR>
|
||
|
||
In the illustration to the right, for example, the <B>P53 tumor suppressor</B> (accession <A HREF="/Structure/pdb/1TUP">1TUP</A>) is bound to double-stranded DNA, as viewed in the free <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> stand-alone program. The three-dimensional structure shows the functional shape of the protein and can be used to infer the specific amino acids that are active in binding to DNA. Here, yellow spheres represent amino acids within 5 Angstroms of the DNA strands. <i>(Click on the image for <A HREF="mmdb_how_to_view_in_cn3d.html#Figure1"><span style="color:#d70000">step by step instructions</span></A> on how to generate that particular view using the stand-alone Cn3D program. The structure can also be viewed in the free <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> web-based 3D viewer (<a href="/Structure/icn3d/full.html?mmdbid=1tup&showanno=1&show2d=1">open 1TUP in iCn3D</a>), where the iCn3D menu option for "<a href="../../icn3d/docs/icn3d_help.html#MenuSelect">Select</a> > <a href="../../icn3d/docs/icn3d_help.html#SelectByDistance">By Distance</a>" can be used to highlight the interaction interfaces.)</i>
|
||
A number of the mutations (allelic variants) observed in patients with Li-Fraumeni syndrome and various cancers appear to have occurred in or near those regions of the protein, based on an <A HREF="mmdb_how_to_view_in_cn3d.html#Figure2"><span style="color:#d70000">alignment</span></A> of the <A HREF="/protein/NP_000537">393 amino acid TP53 protein</A> <!-- (<A HREF="/protein/P04637">P04637</A>) --> discussed in <!-- A HREF="/omim/" --><I>Online Mendelian Inheritance in Man</I> (<A HREF="/omim/?term=191170">OMIM 191170</A>) to the 3D structure's protein sequence data. Together, the sequence data, 3D structure, and phenotypic observations yield a greater understanding of the <B>protein and its biological function</B> than any one of them alone could. Open the structure record (accession <A HREF="/Structure/pdb/1TUP">1TUP</A>) to read more about it, and use either the <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> stand-alone program or the <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> web-based program to interactively view the structure and its corresponding sequence data.<BR><BR>
|
||
|
||
Throughout this help document, the structures of the P53 tumor suppressor (<A HREF="/Structure/pdb/1TUP">1TUP</A>) and prostaglandin-endoperoxide synthase (<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1PTH">1PTH</A>, discussed in the <A HREF="#DatabaseApplications">sequence-structure-function</A> section of this document) are used in search examples and illustrations to show the ways in which the Molecular Modeling database can be searched and to describe the contents and features of a structure record.<BR><BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ============= FOUR_LEVELS_OF_STRUCTURE =============== -->
|
||
|
||
<TR>
|
||
<TD class="NormalText" ALIGN="LEFT" VALIGN="TOP">
|
||
|
||
<A NAME="FourLevelsOfStructure"></A>
|
||
<A NAME="FourLevelsOfProteinStructure"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Four Levels of Protein Structure</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<!-- ===== IMAGE_TO_RIGHT_OF_TEXT_FOUR_LEVELS_OF_STRUCTURE ===== -->
|
||
<A HREF="https://www.genome.gov/genetics-glossary/Protein"><IMG src="images/nhgri_four_levels_of_structure.png" width="400" height="580" border="0" align="right" alt="Image showing the four levels of protein structure: primary, secondary (alpha helices and beta sheets), tertiary, and quaternary. Click on the image to view it on the NHGRI Talking Glossary of Genetic Terms, the source of the image."></A>
|
||
<!-- ===== END_IMAGE_TO_RIGHT_OF_TEXT_FOUR_LEVELS_OF_STRUCTURE ===== -->
|
||
|
||
A linear protein (referred to as the <B>primary structure</B>) consists of <A HREF="/projects/collab/FT/index.html#7.4.3">amino acids</A> with varying chemical properties</A>. Forces of attraction among the amino acids cause regions of the protein molecule to fold into one of two basic shapes, which are referred to as <B>secondary structures</B> and take the shape of <B>alpha-helices</B> and <B>beta-sheets</B> (also known as <B>pleated-sheets</B>). Depending on its length and composition, a single protein molecule can contain one or more secondary structures; for example, some regions of the molecule might fold into alpha-helices while another folds into a beta-sheet. The three-dimensional shape of the complete protein molecule is called its <B>tertiary structure</B>. Some biological molecules are composed of two or more proteins that are assembled into a complex, and the shape of the overall complex is called its <B>quaternary structure</B>. These levels of structure are shown in the illustration to the right.<BR><BR>
|
||
|
||
An example of a biomolecule with a quaternary structure is the human P53 tumor suppressor (accession <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=51571">1TUP</A>). It is composed of three protein molecules, as shown in brown, blue, and pink portions of the illustration for "<A HREF="#WhatIs">what are macromolecular structures?</A>". Open the <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=51571">1TUP</A> record in MMDB, and then click on the "full featured 3D viewer" button in the molecular graphic to <A HREF="/Structure/icn3d/full.html?&mmdbid=103701&bu=1&showanno=1">view 1TUP interactively</A> in the free <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> web-based 3D viewer to see: (a) its linear protein sequences (primary structures); (b) the secondary structures into which each protein molecule folds (alpha helices are shown as green spirals and beta sheets as yellow bands in Cn3D's default view); and (c) how the three proteins come together (tertiary and quaternary structures) to form the biolocially active molecule that binds with DNA. <i>(The 1TUP structure can also be <a href="#MmdbsrvStructureView">downloaded</a> in ASN.1 (Cn3D) format and viewed in the free stand-alone <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> program.)</i>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ================== EXPERIMENTAL_METHODS ================= -->
|
||
|
||
<A NAME="ExperimentalMethods"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Experimental Methods</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
Most structure data are obtained from X-ray crystallography and NMR-spectroscopy. <B>X-ray crystallography</B> determines the arrangement of atoms within a protein by passing X-rays through a crystallized form of the protein and analyzing the resulting X-ray diffraction pattern. This technique provides the highest resolution and usually yields only one model of a structure. <B>Nuclear magnetic resonance (NMR)</B> determines the structure of a protein in solution and generally yields multiple models, which allow for characterization of the biomolecule's motion in solution. An <A HREF="#DataTypes">example of each type of structure</A> is shown in the section of this document on "record types", and additional experimental methods are listed in the <A HREF="#SearchFieldExpMethod">ExpMethod</A> search field of the database.<BR><BR>
|
||
|
||
As an alternative to these experimental methods, some researchers use <B>computational modeling</B> to predict the structure of a protein by simulating the forces that act on each atom in a molecule of known composition. However, this method produces non-experimental models and the least reliable results. For these reasons, the Molecular Modeling Database excludes computationally generated structures or other theoretical models and includes only experimentally determined structures.
|
||
|
||
<!-- To illustrate the ways in which the Molecular Modeling database can be used, the P53 tumor suppressor and peroxidase structures (accessible from the "illustrated example" link above) are used in illustrations and examples threaded through this help document.<BR><BR -->
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ================== DATABASE_APPLICATIONS ================= -->
|
||
|
||
<TR>
|
||
<TD class="NormalText" ALIGN="LEFT" VALIGN="TOP">
|
||
|
||
<A NAME="DatabaseApplications"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>How can 3D structures be used to learn more about proteins and other biomolecules?</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<!-- ===== IMAGE_TO_RIGHT_OF_TEXT_SEQUENCE_STRUCTURE_FUNCTION_1PTH ===== -->
|
||
|
||
<A NAME="SequenceStructureFunctionIllustration"></A>
|
||
<A HREF="mmdb_how_to_align_query_protseq_to_struct.html"><IMG src="images/1PTH_thumbnail_portal.png" width="290" height="475" border=0 align="right" alt="Image depicting the sequence-structure-function relationships that can be revealed by 3-dimensional macromolecular structures. A query protein sequence from human (NP_000953) is aligned to a homologous sheep sequence that has a resolved 3D structure (1PTH), which reveals the inferred structural basis of aspirin activity. Click on the image to view step by step instructions on how to generate this view using the free Cn3D software program."></A>
|
||
|
||
<!-- ===== END_IMAGE_TO_RIGHT_OF_TEXT_SEQUENCE_STRUCTURE_FUNCTION_1PTH ===== -->
|
||
|
||
<A NAME="DatabaseApplicationsRepresentativeStructures"></A>
|
||
|
||
<B>Identify Representative 3D structures for Protein Families:</B>  Because the techniques for resolving 3D structures are not as rapid as sequencing technologies, the number of protein structures available in the <A HREF="/sites/entrez?db=structure">Molecular Modeling Database</A> is smaller than the number of sequences in the <A HREF="/protein/">Protein</A> and <A HREF="/nuccore/">Nucleotide</A> databases. However, a large fraction of all known protein sequences have homologs in the set of resolved 3D structures, and one may often learn more about a protein by examining 3-D structures of its homologs. These can be found by following the <A HREF="#LinksFromProteinToStructure">"Related Structures"</A> link when viewing a protein sequence record, as shown frame B in the <A HREF="mmdb_how_to_search_by_gene.html"><span style="color:#d70000">illustrated example</span> of how to retrieve 3D structures for a gene or product of interest</A>.<BR><BR>
|
||
|
||
<A NAME="DatabaseApplicationsSequenceStructureFunction"></A>
|
||
|
||
<B>Examine Sequence-Structure-Function Relationships:</B>  
|
||
|
||
The sequence-structure relationship of all structures in the Molecular Modeling Database can be interactively explored using the free <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> web-based 3D viewer or the free <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> stand-alone software program. In addition, when structures include a bound chemical or other observed interactions, the function of the biomolecule is elucidated. For example, the <A HREF="mmdb_how_to_align_query_protseq_to_struct.html"><span style="color:#d70000">illustration to the right</span></A> shows the 3-D structure of an ovine prostaglandin H2 synthase protein (<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885">1PTH</A>), which reveals the inferred <!-- A HREF="/sites/entrez?db=pubmed&term=7552725 8121489" --><A HREF="/pubmed/7552725">structural basis of aspirin activity</A>. The homologous human protein (<A HREF="/protein/18104967">NP_000953</A>, prostaglandin-endoperoxide synthase 1) does not yet have a resolved structure but can be aligned to the sheep's protein sequence in Cn3D, and the relationship between the two sequences and corresponding 3D structure can then be examined interactively. Click on the image to view <A HREF="mmdb_how_to_align_query_protseq_to_struct.html"><span style="color:#d70000">step by step instructions</span></A> on how to do this in the stand-alone Cn3D. Or, see an example of <a href="/icn3d/docs/icn3d_help.html#ExampleAlignProteinSequenceToStructure">how to align a protein sequence with unknown structure to a sequence-similar 3D structure using the web-based iCn3D</a>. The <A HREF="/Structure/CN3D/cn3dtut.shtml">Cn3D tutorial</A> and the <A HREF="../../icn3d/docs/icn3d_help.html">iCn3D help document</A> provide additional details on how to use the programs.<BR><BR>
|
||
|
||
<A NAME="DatabaseApplicationsConservedCoreMotifs"></A>
|
||
|
||
<B>View 3D Structures of Conserved Core Motifs:</B>  
|
||
|
||
The <A HREF="../../cdd/cdd.shtml">Conserved Domain Database (CDD)</A>, a related resource maintained by the NCBI <A HREF="../../index.shtml">Structure Group</A>, includes an <A HREF="../../cdd/cdd_help.shtml#CDSource_NCBI_curated">NCBI-curated</A> data set whose goal is to provide insights into how patterns of residue conservation and divergence in a protein family relate to functional properties, and to provide useful links to more detailed information that may help to understand those sequence/structure/function relationships. To achieve this, the curators combine information about conserved domains from multiple sequence alignments with what we can infer from three-dimensional structure and three-dimensional structure superposition. As a result, the NCBI-curated conserved domain records include representations of <A HREF="../../cdd/cdd_help.shtml#NCBI_curated_domains">conserved structural core motifs</A> whenever possible, and the 3D structure images in the domain's <A HREF="../../cdd/cdd_help.shtml#ConservedFeatures">conserved feature</A> summary box link to <A HREF="../../cdd/cdd_help.shtml#CDStructure">specially annotated views of the 3D structures</A> that highlight the conserved feature.<BR><BR>
|
||
|
||
<A NAME="DatabaseApplicationsActiveSites"></A>
|
||
|
||
<B>Identify Putative Active Site Residues:</B>  
|
||
|
||
The free <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> web-based 3D viewer or the free <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> stand-alone software program can be used to <A HREF="mmdb_how_to_view_active_site_residues.html">identify putative active site residues</A>. To do this in the web-based iCn3D, use the menu option for "<a href="../../icn3d/docs/icn3d_help.html#MenuSelect">Select</a> > <a href="../../icn3d/docs/icn3d_help.html#SelectByDistance">By Distance</a>." To do this in stand-alone Cn3D, use the "Show/Hide:Select by Distance" option to highlight amino acids within a specified distance (e.g., 5 Angstroms) of a molecule of interest. Examples using stand-alone Cn3D are shown in the image to the right and in the human P53 Tumor Suppressor protein image shown in "<A HREF="#WhatIs">What are macromolecular structures?</A>". Click on either image to open a separate page with step-by-step instructions on how to generate that view in the stand-alone Cn3D. The <A HREF="/Structure/CN3D/cn3dtut.shtml">Cn3D tutorial</A> and the <A HREF="../../icn3d/docs/icn3d_help.html">iCn3D help document</A> provide additional details on how to use the programs.<BR><BR>
|
||
|
||
The <A HREF="../../cdd/cdd_help.shtml#CDSource_NCBI_curated">NCBI-curated</A> data set in <A HREF="../../cdd/cdd.shtml">CDD</A> also identifies amino acids involved in catalysis and binding whenever possible and describes their function in the <A HREF="../../cdd/cdd_help.shtml#ConservedFeatures">conserved feature</A> summary box of a conserved domain record. The specific amino acids involved in the conserved feature are marked with hash signs (#) in the domain model's multiple sequence alignment and highlighted in <A HREF="../../cdd/cdd_help.shtml#CDStructure">specially annotated 3D structures</A>, when available.<BR><BR>
|
||
|
||
<!-- A NAME="DatabaseApplications_________"></A>
|
||
|
||
<B>_______________:</B>  
|
||
|
||
Text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text.<BR><BR -->
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</P>
|
||
<BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ====== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ############ -->
|
||
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ############### BLUE_HEADER_SECTION_2_UNIQUE_FEATURES ############### -->
|
||
|
||
<A NAME="DatabaseFeatures"></A>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Useful Features of the Molecular Modeling Database</SPAN></TD>
|
||
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############## END_BLUE_HEADER_SECTION_2_UNIQUE_FEATURES ############# -->
|
||
|
||
|
||
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_2_CONTENTS ########### -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
||
<TR>
|
||
<TD class="WhiteCellBlueEdgeAll">
|
||
|
||
<!-- ============ LEVEL_1_UNIQUE_FACILITATE_COMPUTATION ============== -->
|
||
|
||
<BR><BR>
|
||
<A NAME="FacilitateComputation"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Facilitate computation on 3D structure data</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
Uniform <A HREF="#DataProcessing">processing</A> and <A HREF="#DataProcessingValidation">validation</A> of 3D structure data enables a variety of <A HREF="#ComputationalAnalyses">computational analyses</A> within individual structure records and across the complete MMDB database, in order to identify salient features of 3D structures and relationships among them.<BR><BR>
|
||
|
||
The results of the analyses, along with the <A HREF="#DataConnections">connection of structure records</A> to associated data throughout the Entrez system, permit the retrieval of data sets that have certain attributes, as well as the association of proteins that do not yet have resolved 3D structures with those that do. For example, in MMDB it is possible to:<BR><BR>
|
||
|
||
<UL>
|
||
<LI><A HREF="mmdb_how_to_search_by_gene.html">Find structures for a gene/protein product of interest or its homologs.</A></LI>
|
||
<LI><A HREF="mmdb_how_to_search_by_chemical.html">Find 3D structures bound to a specific chemical (e.g., aspirin).</A></LI>
|
||
<!-- LI><A HREF="mmdb_how_to_search_by_small_biopolymer.html">Find 3D structures bound to a specific small biopolymer (e.g., a peptide).</A></LI -->
|
||
<LI><A HREF="mmdb_how_to_align_query_protseq_to_struct.html">Align a query protein to a similar sequence from a 3D structure and interactively view sequence/structure relationships.</A></LI>
|
||
<LI><A HREF="mmdb_how_to_find_similar_structures.html">Identify structures within the database that are similar to each other, regardless of their degree of sequence similarity.</A></LI>
|
||
<!-- LI><A HREF="../../ibis/ibis.cgi">Examine the categories of interactions and binding sites that have been observed across numerous 3D structures that are similar in shape.</A></LI -->
|
||
<LI><A HREF="mmdb_how_to.html">and more...</A></LI>
|
||
</UL>
|
||
|
||
<!-- P class="pad20">In these and other ways, the Structure database is designed to facilitate computation on structual data in order to...</P -->
|
||
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- ============ LEVEL_1_UNIQUE_COMPUTATIONAL_ANALYSES ============== -->
|
||
|
||
<A NAME="ComputationalAnalyses"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Analysis of individual structures and relationships among them</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
A variety of computational analyses are performed during MMDB <A HREF="#DataProcessing">data processing</A> in order to identify salient features of individual 3D structures, and to identify relationships among structures across the database:
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ================ LEVEL_2_UNIQUE_BIOLOGICAL_ANNOTATIONS ============== -->
|
||
|
||
<A NAME="GeometricalFeatures"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
<B>Biological and geometrical features within 3D structures</B> <!-- img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A --></BLOCKQUOTE>
|
||
|
||
<BLOCKQUOTE><BLOCKQUOTE>
|
||
The primary content of 3D structure records are the spatial (x,y,z) coordinates of each atom in the structure. The NCBI <A HREF="#DataProcessing">data processing</A> procedure analyzes that information to identify: (1) distinct <A HREF="#DataProcessingBiologicalForms">biological units</A> within the structure; (2) <A HREF="#DataProcessingInteractions">interactions</A> among its molecular components; and (3) <A HREF="#FourLevelsOfStructure">secondary structures</A> (<B>alpha helices</B>, <B>beta strands</B>) as well as <!-- A HREF="../mmdb.shtml#3D_Domains" --><A HREF="#DataProcessing3dDomains">3D domains</A><!-- (<A HREF="../../cdd/cdd_help.shtml#CDWhat"><I><span style="color:#d70000">illustrated example</span></I></A>) --> within individual protein molecules. This information is then used in further analyses to identify <A HREF="#EvolutionaryRelationships">evolutionary relationships</A> and <A HREF="#FunctionalRelationships">functional relationships</A> among 3D structures.<BR><BR>
|
||
|
||
<!-- {In addition, the data processing procedure calculates distances between atoms in the structure's <A HREF="#MmdbsrvMolecularComponents">molecular components</A> (protein molecules, RNA molecules, DNA molecules, bound chemicals) to infer <B>interactions</B> among the components, <B>biological units</B> within the structures (oligomeric forms), and <B>binding sites</B>.} -->
|
||
|
||
<!-- UL>
|
||
<LI><P class="pad10">test1</P></LI>
|
||
<LI><P class="pad10">test2</P></LI>
|
||
<LI><P class="pad10">test3</P></LI>
|
||
<UL>
|
||
<LI><P class="pad10">test3a</P></LI>
|
||
<LI><P class="pad10">test3b</P></LI>
|
||
<LI><P class="pad10">test3c</P></LI>
|
||
</UL>
|
||
</UL -->
|
||
|
||
</BLOCKQUOTE></BLOCKQUOTE>
|
||
|
||
<!-- =========== LEVEL_2_UNIQUE_CONSERVED_DOMAIN_ANNOTATIONS ============ -->
|
||
|
||
<A NAME="ConservedDomainAnnotations"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
<B>Conserved protein domain annotations</B> <!-- img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A --></BLOCKQUOTE>
|
||
|
||
<BLOCKQUOTE><BLOCKQUOTE>
|
||
Each protein sequence in a 3D structure is compared against the <A HREF="../../cdd/cdd.shtml">Conserved Domain Database</A> using the <A HREF="../../cdd/cdd_help.shtml#CDSearch_help_contents">CD-Search</A> (<A HREF="../../cdd/cdd_help.shtml#RPSBWhat">RPS-BLAST</A>) tool to identify the <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A> within the protein and therefore infer its function.<BR><BR>
|
||
|
||
Structure data are also incorporated into <A HREF="../../cdd/cdd_help.shtml#NCBI_curated_domains">NCBI-curated conserved domains</A> whenever possible in order to combine information that has been derived from multiple sequence alignments with what we can infer from three-dimensional structure and three-dimensional structure superposition, providing insights into how patterns of residue conservation and divergence in a protein family relate to functional properties. These sequence-structure associations also make it possible to <A HREF="#DatabaseApplicationsConservedCoreMotifs">view 3D structures of conserved core motifs</A> and <A HREF="#DatabaseApplicationsActiveSites">identify putative active site residues</A>.
|
||
|
||
<!-- Structure data are also incorporated into <A HREF="../../cdd/cdd_help.shtml#NCBI_curated_domains">NCBI-curated conserved domains</A> whenever possible in order to refine multiple sequence alignments that reveal protein functional units conserved in molecular evolution and identify specific <A HREF="../../cdd/cdd_help.shtml#ConservedFeatures">amino acids involved in catalysis and binding</A>. -->
|
||
</BLOCKQUOTE></BLOCKQUOTE>
|
||
|
||
|
||
<!-- ============ LEVEL_2_UNIQUE_EVOLUTIONARY_RELATIONSHIPS ============ -->
|
||
|
||
<A NAME="EvolutionaryRelationships"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
<B>Evolutionary relationships among 3D structures</B> <!-- img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A --></BLOCKQUOTE>
|
||
|
||
<BLOCKQUOTE><BLOCKQUOTE>
|
||
The <A HREF="../../VAST/vast.shtml">Vector Alignment Seach Tool (VAST)</A> computer algorithm was developed to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison.<BR><BR>
|
||
|
||
To do this, VAST identifies <A HREF="#DataProcessingGeometricalFeatures">3D domains</A> (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other structures that contain similarly shaped protein molecules. This output, referred to as "Original VAST," reflects comparisons between individual protein molecules, which can share a similar shape along their entire length, or only along a fraction of their length, such as a single 3D domain.<BR><BR>
|
||
|
||
In addition, <A HREF="../../vastplus/vastplus.cgi">VAST+</A>, an expanded version of the program, finds macromolecular structures that have similarly shaped <A HREF="#DataProcessingBiologicalForms">biological units</A> (also referred to as "biounits"), not just those that share similarly shaped individual protein molecules or fragments.<BR><BR>
|
||
|
||
|
||
VAST and VAST+ are applied during <A HREF="#DataProcessing">data processing</A> to identify similar 3D structures for every protein in MMDB, and the pre-computed results are accessible via "<!-- A HREF="#LinksSimilarStructures" --><!-- A HREF="#LinksRelatedStructures" --><!-- A HREF="#MmdbsrvRelatedStructures" --><A HREF="#MmdbsrvSimilarStructures">Similar Structures: VAST+</A>" links on the <!-- MMDB <A HREF="#SearchResults">search results</A> and --><A HREF="#SummaryPage">structure summary</A> pages.<BR><BR>
|
||
|
||
The <A HREF="../../vastplus/docs/vastplus_help.html">VAST+ help document</A> provides details about the <A HREF="../../vastplus/docs/vastplus_help.html#Compare">differences between VAST and VAST+</A>, an <A HREF="../../vastplus/docs/vastplus_help.html#IllustratedExamples">illustrated example of VAST+ results</A>, and an <A HREF="../../vastplus/docs/vastplus_help.html#OriginalVASTDisplay">illustrated example of original VAST results</A>.<BR><BR>
|
||
|
||
|
||
<I>(The <A HREF="../../VAST/vastsearch.html">VAST Search</A> page can also be used to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors.)</I>
|
||
</BLOCKQUOTE></BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- ============ LEVEL_2_UNIQUE_FUNCTIONAL_RELATIONSHIPS ============ -->
|
||
|
||
<A NAME="FunctionalRelationships"></A>
|
||
|
||
<!-- BLOCKQUOTE>
|
||
<B>Functional relationships among 3D structures</B> [<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>]</BLOCKQUOTE>
|
||
|
||
<BLOCKQUOTE><BLOCKQUOTE>
|
||
The NCBI <A HREF="../../ibis/ibis.cgi">Inferred Biomolecular Interaction Server (IBIS)</A> was developed categorize interactions observed across numerous experimentally-determined structures that are similar in 3D shape (i.e., across [<A HREF="../../VAST/vast.shtml">]VAST "<A HREF="#LinksSimilarStructures">Similar Structures</A>"), and to infer/predict interacting partners and binding sites by homology. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation.<BR><BR>
|
||
|
||
Each protein in MMDB is analyzed using IBIS and similar 3D structures are clustered based on sequence and structural conservation in their binding sites. For example, the <A HREF="/Structure/ibis/ibis.cgi?search=1tup&page=init">IBIS results for the human P53 Tumor Suppressor (1TUP)</A> show four clusters of similar 3D structures, each of which is labeled with the name of the conserved domain (P53, Polyoma_lg_T_C, ANK, and SH3) found in cluster members. Open the "+" beside a cluster to view its details, including a list of 3D structures in the cluster. Click on the PDB accesssion of any cluster member to view its complete structure record, the chemicals to which it is bound (if applicable), etc.[In this example, members of all clusters bind to Zinc. However, IBIS results for other structures (e.g., 1PTH) will reveal clusters of similar 3D structures that bind to various chemicals (e.g., salicylic acid, Diclofenac).]
|
||
</BLOCKQUOTE></BLOCKQUOTE -->
|
||
|
||
|
||
<!-- ==== LEVEL_1_UNIQUE_INTERACTIVELY_VIEW_SEQUENCE_STRUCTURE_RELATIONSHIPS -->
|
||
|
||
<A NAME="SequenceStructureRelationship"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Interactive views of sequence-structure relationships</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
All structures in MMDB can be viewed with the the free <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A> web-based 3D viewer or the free <A HREF="../../CN3D/cn3d.shtml"><B>Cn3D</B></A> stand-alone software program, which were developed as companion resources to MMDB in order to visualize three-dimensional structures with an emphasis on interactive examination of sequence-structure relationships. Both iCn3D and Cn3D can <B>simultaneously display</B> a <B>3D structure</B> and its <B>corresponding sequence data</B>, and allow you to <B>select items of interest</B> (e.g., entire protein or nucleotide molecules, spans of sequence data, or individual amino acids or nucleotides, as desired) <B>in either view</B> in order to <B>examine their location in both views</B>. An illustrated example of the stand-alone Cn3D display is shown featuring the <A HREF="mmdb_how_to_view_in_cn3d.html#Figure1">human P53 tumor suppressor</A>, in which amino acids within 5 Angstroms of the bound DNA are highlighted in yellow in Cn3D's structure and sequence view windows.<BR><BR>
|
||
|
||
Proteins with similar sequence data can also be imported into either <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> or <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> and aligned to the structure's sequence data, as shown in the illustrated example showing Cn3D's alignment of <A HREF="mmdb_how_to_align_query_protseq_to_struct.html">human prostaglandin endoperoxide synthase 1 to a sheep homolog with a resolved 3D structure.</A><BR><BR>
|
||
|
||
<A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> and <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> can also be used to display superpositions of geometrically similar structures (i.e., <!-- A HREF="../../VAST/vast.shtml" -->VAST <A HREF="#LinksSimilarStructures">Similar Structures</A>), conserved core motifs identified in conserved domains, and <A HREF="mmdb_how_to_view_in_cn3d.html#Method2">newly resolved structures in PDB format</A> that are not yet present in MMDB.<BR><BR>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ================ LEVEL_1_UNIQUE_DATA_CONNECTIONS ================= -->
|
||
|
||
<A NAME="DataConnections"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Connections between 3D structure records and associated literature, molecular, and chemical data</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
For each structure in MMDB, the <A HREF="#DataProcessing">data processing</A> procedure identifies associated literature, molecular, and chemical data throughout the <A HREF="/sites/gquery">Entrez</A> system, and then establishes connections among those data sets. These related data are accessible as <A HREF="#DocSumLinks">Links</A> on the MMDB <A HREF="#SearchResults">search results</A> and <A HREF="#SummaryPage">structure summary</A> pages.<!-- and can include the following, as available for an individual structure: -->
|
||
|
||
<!-- UL>
|
||
<LI>protein and/or nucleotide sequence data derived from the structure</LI>
|
||
<LI>functional (conserved domains) and geometrical (3D domains) classification of the proteins</LI>
|
||
<LI>physicochemical and biological properties of bound chemicals</LI>
|
||
<LI>biosystems in which the 3D structure has been identified as a component</LI>
|
||
<LI>literature about the structure</LI>
|
||
<LI>additional information associated with the structure such as gene or disease information in Online Mendelian Inheritance in Man (OMIM), when available</LI>
|
||
<LI>additional proteins in Entrez that are similar in sequence (as determined by <A HREF="https://blast.ncbi.nlm.nih.gov/">BLAST</A>) or 3D shape (as determined by <A HREF="../../VAST/vast.shtml">VAST</A>) to a protein structure of interest</LI>
|
||
</UL -->
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
|
||
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_2_CONTENTS ====== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_2_CONTENTS ############ -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ################ BLUE_HEADER_SECTION_3_CONTENT_OF_DATABASE ############### -->
|
||
|
||
<A NAME="DatabaseContent"></A>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Content of the Molecular Modeling Database</SPAN></TD>
|
||
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############## END_BLUE_HEADER_SECTION_3_CONTENT_OF_DATABASE ############# -->
|
||
|
||
|
||
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ########### -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
||
<TR>
|
||
<TD class="WhiteCellBlueEdgeAll">
|
||
|
||
<!-- ================= LEVEL_1_SOURCE_DATABASES ==================== -->
|
||
|
||
<A NAME="SourceDatabases"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Source Database</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
The <A HREF="../mmdb.shtml">Molecular Modeling DataBase (MMDB)</A> is a database of experimentally determined three-dimensional biomolecular structures, and is also referred to as the <SPAN class="ThumbText"><A HREF="/structure"><B>Entrez Structure</B></A></SPAN> database. It is a subset of three-dimensional structures obtained from the <SPAN class="ThumbText"><A HREF="http://www.rcsb.org/pdb/"><B>RCSB Protein Data Bank (PDB)</B></A></SPAN>, excluding theoretical models. The <A HREF="#DataProcessing">data processing</A> procedure at NCBI results in the addition of a number of <A HREF="#DatabaseFeatures">useful features</A> that facilitate computation on the data and link them to many other data types in the <SPAN class="ThumbText"><A HREF="/sites/gquery/"><B>Entrez</B></A></SPAN> system.<BR><BR>
|
||
|
||
Each MMDB record cross-references the <B>source PDB record</B> from which it was derived (i.e., the <A HREF="#SummaryPage">MMDB summary page</A> for a structure displays both its <A HREF="#MmdbsrvMMDBID">MMDB ID</A> and the corresponding <A HREF="#MmdbsrvPDBID">PDB ID</A>). If an MMDB record represents a <A HREF="#DataProcessingMergeSplitFiles">structure that was merged from two or more PDB split files</A>, then the summary page will show the PDB IDs of all the source PDB records that compose the merged structure.<BR><BR>
|
||
|
||
MMDB contains various <A HREF="#DataTypes">record types</A>, reflecting various <A HREF="#DataTypeExperimentalMethods">experimental methodologies</A> such as X-ray crystallography and Nuclear Magnetic Resonance (NMR), and various <A HREF="#DataTypeMolecularComponents">molecule types</A> such as proteins, DNA, and RNA, with or without bound chemicals.<BR><BR>
|
||
|
||
The content of an individual structure record reflects the data provided by the submitter, and the literature associated with a structure record provides more details about it. Note that various data submitters might use different terminology to describe the same gene or protein (for example, some might use the term "suppressor" while others use the term "inhibitor"), so it is often helpful to include synonyms, such as acronyms, full spellings, and disease names, if appropriate, when searching the database (see <A HREF="#SearchTips">search tips</A>).<BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
|
||
<!-- ================= LEVEL_1_DATA_PROCESSING ==================== -->
|
||
|
||
<A NAME="DataProcessing"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>How are the data processed at NCBI?</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
|
||
<!-- ============ MINI_TOC_FOR_DATA_PROCESSING ============== -->
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
| <A HREF="#DataProcessingValidation">validation</A> |
|
||
<A HREF="#DataProcessingDeposition">deposit sequence and chemical data</A> |
|
||
<A HREF="#DataProcessingBiologicalForms">identify biological units (oligomeric states</A>, example: <A HREF="#DataProcessingHumanHemoglobinExamples">hemoglobin</A>) |
|
||
<A HREF="#DataProcessingMergeSplitFiles">merge PDB split files</A> (examples: <A HREF="#DataProcessingMergeSplitFilesExample_1VU0_ViralCapsidAav6">viral capsid</A>, <A HREF="#DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault">rat liver vault</A>, <A HREF="#DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel">ribosome</A>) |
|
||
<A HREF="#DataProcessingInteractions">identify interactions</A> |
|
||
<A HREF="#DataProcessingGeometricalFeatures">identify geometrical features</A> |
|
||
<A HREF="#DataProcessingGenes">identify the gene that corresponds to each protein</A> |
|
||
<A HREF="#DataProcessingRelatedStructures">identify relationships among 3D structures</A> |
|
||
<A HREF="#DataProcessingCreateLinks">create links to associated data</A> |
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ========== END_MINI_TOC_FOR_DATA_PROCESSING ============ -->
|
||
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<!-- A NAME="DataProcessingIntro"></A>
|
||
<When <A HREF="http://www.rcsb.org/pdb/">PDB</A> structure records are imported into MMDB, the following procedures are carried out:<BR><BR>
|
||
<P class="indent20 MicroText"> </P -->
|
||
|
||
<!-- =================== DATA_PROCESSING_VALIDATION ============ -->
|
||
|
||
<A NAME="DataProcessingValidation"></A>
|
||
<A NAME="DataProcessingContentValidation"></A>
|
||
<A NAME="ContentValidation"></A>
|
||
<P><B>Content Validation</B>:<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
<BR>
|
||
|
||
<P class="indent20">When <A HREF="http://www.rcsb.org/pdb/">PDB</A> structure records are imported into MMDB, the information in each structure record is reorganized and validated in a way that enables cross-referencing between the chemistry and the three-dimensional structure of macromolecules. While the PDB data model provides an elegant and concise description of a crystal structure, there is no one-to-one correspondence between a site, a structure, and an atom in the chemical sense. MMDB provides this chemical information in an explicit manner. Its data specification includes a description of a biopolymer's spatial structure, a description of how it is organized chemically, and a set of pointers linking the two.</P>
|
||
|
||
<UL>
|
||
<LI>The first step in creating MMDB is getting an accurate sequence that is consistent with the atom site coordinates in PDB. For example: <!-- For example, if the structure's atomic coordinates reveal the presence of a larger number of amino acids than listed in the SEQRES records of the original PDB file, MMDB will derive the biopolymer sequence from the atomic coordinates and not from the original SEQRES records. The derived biopolymer sequence will then appear in the MMDB record, and in the SEQRES records of the <A HREF="#MmdbsrvSavePDBformat">PDB-formatted</A> file <A HREF="#MmdbsrvSave"><B>saved</B></A> from the MMDB database.--></LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>The SEQRES records in an original PDB file are generally intended to represent the molecule that was purified, crystallized, and measured. However, <!-- not all of the amino acids can be resolved experimentally, -->it might not have been possible to experimentally resolve the atomic coordinates for all of the amino acids in some structures, especially in flexible regions of proteins such as N- and C- terminals. In addition, sometimes the atomic coordinates might indicate the presence of additional residues not listed in the SEQRES records. In the latter case, MMDB derives the biopolymer sequence from the atomic coordinates and not from the original SEQRES records. The derived biopolymer sequence will then appear in the MMDB record, and in the SEQRES records of the <A HREF="#MmdbsrvSavePDBformat">PDB-formatted</A> file <A HREF="#MmdbsrvSave"><B>saved</B></A> from the MMDB database.</LI><BR><BR>
|
||
|
||
<LI>Some PDB records may have discontinous residue numbers, which exist in a free text field. MMDB assigns a consecutive series of positive integers to residues in biopolymers, using a numerical data field. This ensures correspondence between the residue numbers in the structure file and those in the corresponding <A HREF="#DataProcessingDeposition">protein and/or nucleotide sequence</A> records.</LI>
|
||
|
||
</UL><BR>
|
||
|
||
<LI>The second step is to construct a complete chemical graph for the molecule, representing all bonds and chirality. An important component of this second step matches the amino acid and nucleotide groups defined by PDB against a dictionary that defines all bond and atom types. <!-- {example of what can change in the record and why?} --></LI><BR><BR>
|
||
|
||
<LI>The third and final step is to recover disorder information in the structure.</LI>
|
||
</UL>
|
||
|
||
<P class="indent20"><I>(Note: Because such changes may occur during data processing, the content of a <A HREF="#MmdbsrvSavePDBformat">PDB-formatted</A> file that you <A HREF="#MmdbsrvSave"><B>save</B></A> from the MMDB database might differ from the original PDB file.<!-- if you <A HREF="#MmdbsrvSave"><B>save</B></A> a <A HREF="#MmdbsrvSavePDBformat">PDB-formatted</A> file from the MMDB database, its content might differ from the original PDB file. -->)</I></P>
|
||
|
||
<!-- P class="indent20 MicroText"> </P -->
|
||
<BR>
|
||
|
||
<!-- ================= DATA_PROCESSING_DEPOSITION ============ -->
|
||
|
||
|
||
<A NAME="DataProcessingDeposition"></A>
|
||
<P><B>Deposit sequence and chemical data into <A HREF="/sites/gquery/">Entrez</A> <A HREF="/protein/">Protein</A>, <A HREF="/nuccore/">Nucleotide</A>, and <A HREF="https://pubchem.ncbi.nlm.nih.gov/">PubChem</A> databases</B>:<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
<BR>
|
||
|
||
<P class="indent20">In addition to providing the spatial (x,y,z) coordinates of every atom in a 3D macromolecular structure, a structure record includes the sequence data for each <A HREF="#MmdbsrvMolecularComponents">component</A> nucleotide (DNA, RNA) and/or protein molecule. As part of MMDB <A HREF="#DataProcessing">data processing</A>, the sequence data for each molecule are deposited into the <A HREF="/nuccore/">Entrez Nucleotide</A> or <A HREF="/protein/">Entrez Protein</A> database, as appropriate. The data processing procedures for those databases, in turn, identify relationships (i.e., similarities) among the sequence data from 3D structures and the other sequences in those databases, facilitating the <A HREF="#DatabaseApplications">use of 3D structure data to learn more about proteins and other biomolecules</A>.<BR><BR>
|
||
|
||
A structure record may also include bound chemicals. Data records for those chemicals are deposited into the <A HREF="/sites/entrez?db=pcsubstance">PubChem Substance</A> database, and then linked to corresponding records in the non-redundant, curated <A HREF="/sites/entrez?db=pccompound">PubChem Compound</A> database. <!-- {Should we include additional, technical details about how this is done?} --> This makes it possible, for example, to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D protein structures bound to a specific chemical (e.g., aspirin)</A>, even if submitters of 3D structures used various names or abbreviations for a given chemical.
|
||
|
||
<!-- As described in the sample <A HREF="#SummaryPage">structure summary page</A> later in this document, a structure record can contain various <A HREF="#MmdbsrvMolecularComponents">molecular components</A>, which may include biopolymers ([<A HREF="#MmdbsrvMolecularComponents">]<A HREF="#MmdbsrvProteins">protein molecule</A>, <A HREF="#MmdbsrvNucleotides">DNA, RNA molecules</A>) and <A HREF="#MmdbsrvChemicals">chemicals</A>. --></P>
|
||
|
||
<P class="indent20 NormalText"> </P>
|
||
|
||
|
||
<!-- ============ DATA_PROCESSING_BIOLOGICAL_FORMS ============ -->
|
||
|
||
<A NAME="DataProcessingBiologicalForms"></A>
|
||
<A NAME="BiologicalForm"></A>
|
||
<A NAME="DataProcessingBiologicalUnit"></A>
|
||
<A NAME="BiologicalUnit"></A>
|
||
<A NAME="BiologicalUnits"></A>
|
||
<A NAME="BioUnit"></A>
|
||
<A NAME="BioUnits"></A>
|
||
<A NAME="Biounit"></A>
|
||
<A NAME="Biounits"></A>
|
||
|
||
<P><B>Identify biological units (oligomeric states)</B>:<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
|
||
<!-- ======== MINI_TOC_FOR_DATA_PROCESSING_BIOLOGICAL_FORMS ========== -->
|
||
|
||
<!-- P class="indent40" -->
|
||
<BLOCKQUOTE>
|
||
|
||
<A HREF="#DataProcessingBiologicalFormsOverview">what is a biological unit?</A> |
|
||
<A HREF="#DataProcessingBiologicalFormsExamples">asymmetric unit → biological unit</A> (example: <A HREF="#DataProcessingHumanHemoglobinExamples">hemoglobin </A>) <BR><A HREF="#DataProcessingBiologicalFormsProcedures"><B>procedures to identify biological unit</B></A>: <A HREF="#DataProcessingBiologicalFormsRemark350">author/software determination</A>,
|
||
<A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">transformations from crystallographic symmetry</A>,
|
||
<A HREF="#DataProcessingBiologicalFormsTypeClassification">identify distinct biological units</A>,
|
||
<A HREF="#DataProcessingBiologicalFormsMergeSplitFiles">note about biological units in merged PDB split files</A> |
|
||
<A HREF="#DataProcessingBiologicalFormsAdditionalNotes">technical note about asymmetric unit</A>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ====== END_MINI_TOC_FOR_DATA_PROCESSING_BIOLOGICAL_FORMS ======== -->
|
||
|
||
<A NAME="DataProcessingBiologicalFormsOverview"></A>
|
||
<P class="indent20"><B>What is a biological unit?</B><BR><BR>
|
||
|
||
The <B>biochemically active form of a biomolecule</B> can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules<!-- (as in the <A HREF="/sites/entrez?cmd=search&db=structure&term=2XFZ[accn]+OR+2XG0[accn]+OR+2XG1[accn]+OR+2XG2[accn]">ribosome</A>) -->, and is referred to as "<B>biological unit</B>" <!-- or <B>biounit</B --> for brevity.<BR><BR>
|
||
|
||
The <B>raw data</B> present structure records resolved by x-ray crystallography or neutron diffraction of a crystal are often casually referred to as the "<B>asymmetric unit</B>." These data can represent either: (a) the <B>complete</B> biological unit, (b) a <B>portion</B> of the biological unit, or (c) <B>multiple</B> copies of the biological unit, as in the <A HREF="#DataProcessingHumanHemoglobinExamples">human hemoglobin examples</A> shown below. Authors of structure records use programs such as <A HREF="http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html">PISA</A> <!-- or <A HREF="http://www.ebi.ac.uk/pdbe/pqs/">PQS</A --> to identify the biological unit within a structure record. If multiple interpretations of the biological unit exist, the author may choose to annotate the various interpretations in their record. The MMDB <A HREF="#DataProcessing">data processing pipeline</A> applies several <A HREF="#DataProcessingBiologicalFormsProcedures">procedures to identify a structure's biological unit(s)</A> and displays it by default on a <A HREF="#SummaryPage">structure summary</A> page. <I>(See <A HREF="#DataProcessingAsymmetricUnit">technical note</A> about asymmetric unit.)</I><BR><BR>
|
||
|
||
<!-- As of May 2011, -->The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records resolved by x-ray crystallography or neutron diffraction of crystals. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>, or it represents multiple copies of the biological unit.<!-- {{Biological unit data is now provided for all structure records, with the exception of merged split files and very large structures. The option to view an asymmetric unit appears only if the asymmetric unit is different from the biological unit. If it is the same, the summary page will only display the thumbnail for the biological unit. atomic spatial coordinates and protein and/or nucleotide sequences}} --><BR><BR>
|
||
|
||
Additionally, some structures exceed the size limits implicit to the PDB file format and are therefore <B>split</B> by PDB into several files. In those cases, the biological unit might be spread across multiple PDB files. The MMDB data processing pipeline <A HREF="#DataProcessingMergeSplitFiles"><B>merges</B> the split files</A> into a single structure record. In such cases, "<A HREF="#AsymmetricUnit"><B>asymmetric unit</B></A>" is the only <A HREF="#MmdbsrvDisplayOptions">display option</A> for <A HREF="#DataProcessingMergeSplitFiles">merged PDB split files</A> from <I>crystallographic studies</I>, because the <A HREF="#DataProcessingBiologicalForms"><B>biological unit</B></A> of the complete structure is not specified in a computer readable way in the PDB source files. The <A HREF="#SummaryPage">structure summary</A> page for a merged crystallographic structure therefore simply uses the label of "<!-- A HREF="#DataProcessingAsymmetricUnit" -->asymmetric unit" above the molecular graphic, because it represents the unification of raw data from the original PDB files. The asymmetric unit can represent the structure's complete biological unit, a portion of the biological unit, or multiple copies of the biological unit. In the case of structures resolved by <I>electron microscopy (EM)</I> or <I>nuclear magnetic resonance (NMR)</I>, the term "asymmetric unit" does not apply, and the term "biological unit" is shown instead on the summary page for a merged structure from either of those technologies. Please refer to the corresponding publication for a structure, if/as available, for the author's description of its biologically active form.</I>
|
||
</P>
|
||
<BR>
|
||
|
||
<!-- ====== DATA_PROCESSING_BIOLOGICAL_FORMS_HUMAN_HEMOGLOBIN_EXAMPLE ====== -->
|
||
|
||
<A NAME="DataProcessingBiologicalFormsExamples"></A>
|
||
<A NAME="DataProcessingHumanHemoglobinExamples"></A>
|
||
<P class="indent20 MiniText"> </P>
|
||
|
||
<P class="indent20">
|
||
|
||
<B>Asymmetric unit (raw data) → Biological unit (default display)</B><img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A><BR><BR>
|
||
|
||
<B>Example:</B> -- As an example of the varying degrees to which a biological unit can be represented by the raw data in a structure record, compare the following records for <B>human hemoglobin</B>. Each one contains the spatial coordinates and sequence data for a different number of protein molecules, yet the fundamental <B>biological unit</B> in all three structures is a <B>tetramer</B> consisting of two alpha, two beta subunits, and four heme groups. By default, an MMDB <A HREF="#SummaryPage">structure summary page</A> displays the biological unit:<!-- , with <A HREF="#MmdbsrvDisplayOptions">options</A> to view <A HREF="#DataProcessingBiologicalFormsTypeClassification">additional biological units (if available) and/or the asymmetric unit. --><BR><BR>
|
||
|
||
</P>
|
||
|
||
<A NAME="BiologicalUnitIllustration"></A>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="0">
|
||
<TR>
|
||
<TD width="20"> </TD>
|
||
<TD>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" WIDTH="700" border="0" class="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" class="format1H" colspan="3"><A HREF="#DataProcessingAsymmetricUnit">ASYMMETRIC UNIT</A> (RAW DATA)<BR>IN THREE DIFFERENT STRUCTURE RECORDS FOR HUMAN HEMOGLOBIN:</TD>
|
||
<TD valign="center" align="center" width="14" class="format1H"><IMG SRC="../../IMG/arrow_red_right1.png" WIDTH="12" HEIGHT="20" BORDER="0" ALT="right arrow"></TD>
|
||
<TD valign="top" class="format1H">BIOLOGICAL UNIT <BR>IS SIMILAR IN ALL:</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
|
||
<TD valign="top" class="format1A"><A NAME="DataProcessingHumanHemoglobinExample1"></A>PDB ID: <!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2DN2" --><B>2DN2</B><BR>MMDB ID: <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=39206&dps=2"><!-- A HREF="/structure/39206" --><B>39206</B></A></TD>
|
||
|
||
<TD valign="top" class="format1A"><A NAME="DataProcessingHumanHemoglobinExample2"></A>PDB ID: <!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=1LFT" --><B>1LFT</B><BR>MMDB ID: <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=20898&dps=2"><!-- A HREF="/structure/20898" --><B>20898</B></A></TD>
|
||
|
||
<TD valign="top" class="format1A"><A NAME="DataProcessingHumanHemoglobinExample3"></A>PDB ID: <!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=1LFL" --><B>1LFL</B><BR>MMDB ID: <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=20896&dps=2"><!-- A HREF="/structure/20896" --><B>20896</B></A></TD>
|
||
|
||
<TD valign="center" align="center" width="14" class="format1H" rowspan="2"><IMG SRC="../../IMG/arrow_red_right1.png" WIDTH="12" HEIGHT="20" BORDER="0" ALT="right arrow"></TD>
|
||
|
||
<TD valign="bottom" class="format1B">The MMDB <A HREF="#SummaryPage">summary page</A> for each record displays the biological unit by default:</TD>
|
||
|
||
</TR>
|
||
|
||
<TR>
|
||
|
||
<TD valign="top" class="format1B"><A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=39206&dps=2"><IMG SRC="images/human_hemoglobin_example1_2DN2_asymmetric_unit_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="3D view of the raw data for human hemoglobin submitted in PDB record 2DN2, which contains a complete copy of the structure's biological unit (in this case, a tetramer). Click on the thumbnail to open the structure record in MMDB, where you can launch an interactive 3D view and then color by molecule, as shown here."></A></TD>
|
||
|
||
<TD valign="top" class="format1B"><A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=20898&dps=2"><IMG SRC="images/human_hemoglobin_example2_1LFT_asymmetric_unit_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="3D view of the raw data for human hemoglobin submitted in PDB record 1LFT, which contains half of the structure's biological unit (that is, half of the hemoglobin tetramer). Click on the thumbnail to open the asymmetric unit view in MMDB, where you can choose to view the biological unit and/or launch an interactive 3D view, and then color by molecule as shown here."></A></TD>
|
||
|
||
<TD valign="top" class="format1B"><A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=20896&dps=2"><IMG SRC="images/human_hemoglobin_example3_1LFL_asymmetric_unit_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="3D view of the raw data for human hemoglobin submitted in PDB record 1LFL, which contains two copies of the structure's biological unit. Click on the thumbnail to open the asymmetric unit view in MMDB, where you can choose to view the biological unit and/or launch an interactive 3D view, and then color by molecule as shown here."></A></TD>
|
||
|
||
<TD valign="bottom" class="format1B"><IMG SRC="images/human_hemoglobin_biological_form_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="3D view of the biological unit (tetramer) of human hemoglobin."></TD>
|
||
|
||
</TR>
|
||
|
||
<TR>
|
||
|
||
<TD valign="top" class="format1B"><B>Complete</B> tetramer (two alpha subunits and two beta subunits) of human hemoglobin</TD>
|
||
|
||
<TD valign="top" class="format1B"><B>Half</B> of the tetramer (one alpha subunit and one beta subunit)<BR><BR>
|
||
<I>(Although the raw data in this structure record represents only half of the tetramer, MMDB's automated <A HREF="#DataProcessing">data processing</A> procedure applies the tranformations derived from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A> to generate the other half, as shown in the corresponding biological unit.)</I></TD>
|
||
|
||
<TD valign="top" class="format1B"><B>Two copies</B> of the tetramer (four alpha subunits and four beta subunits)</TD>
|
||
|
||
<TD valign="center" align="center" width="14" class="format1H"> </TD>
|
||
|
||
<TD valign="top" class="format1B"><B>Tetramer</B> with <B>two alpha</B> subunits, <B>two beta</B> subunits, and <B>four heme</B> groups. A corresponding schematic shows the <A HREF="#MmdbsrvThumbnailSchematic">interactions</A> among the components:<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="5" border="0">
|
||
<A HREF="#MmdbsrvThumbnailSchematic"><IMG SRC="images/human_hemoglobin_biological_form_interactions_schematic.png" WIDTH="163" HEIGHT="163" BORDER="0" ALT="Interaction schematic for the human hemoglobin tetramer, showing protein molecules as circles and heme groups as diamonds, with lines indicating interactions with at least 5 contacts a distance of 4 Angstroms or less between the heavy atoms."></A>
|
||
<BR>
|
||
The summary page also provides <A HREF="#MmdbsrvDisplayOptions">display options</A> to view all biological units (if applicable) or the asymmetric unit, if desired.</TD>
|
||
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<P class="indent20 NormalText"> </P>
|
||
|
||
<!-- ====== END_DATA_PROCESSING_BIOLOGICAL_FORMS_HUMAN_HEMOGLOBIN_EXAMPLE ====== -->
|
||
|
||
<!-- ========= DATA_PROCESSING_BIOLOGICAL_FORMS_PROCEDURES =========== -->
|
||
|
||
<A NAME="DataProcessingBiologicalFormsProcedures"></A>
|
||
<A NAME="DataProcessingBiologicalUnitsProcedures"></A>
|
||
|
||
<P class="indent20 MiniText"> </P>
|
||
|
||
<P class="indent20 NormalText"><B>Procedures to identify the biological unit(s) within a structure record</B>:<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
<BR>
|
||
|
||
<BLOCKQUOTE>
|
||
<A HREF="#DataProcessingBiologicalFormsRemark350">author/software determination</A> | <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">transformations from crystallographic symmetry</A> | <A HREF="#DataProcessingBiologicalFormsTypeClassification">comparison of biological units</A> | <A HREF="#DataProcessingBiologicalFormsMergeSplitFiles">note about biological units in merged PDB split files</A>
|
||
</BLOCKQUOTE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingBiologicalFormsRemark350"></A><A NAME="DataProcessingRemark350"></A><B>author and/or software determination</B><!-- B>parse REMARK 350 <BR>to identify biological unit</B --></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">The "<B>REMARK 350</B>" record of a PDB source file specifies the <A HREF="#DataProcessingBiologicalForms">biological unit (oligomeric state)</A> of the structure and lists the protein molecules of which it is composed. The REMARK 350 also indicates how the biological unit was determined -- by the <B>author</B> and/or a <B>software</B> program, and if the latter, which software program was used (e.g., <A HREF="http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html">PISA</A>, <A HREF="http://www.ebi.ac.uk/pdbe/pqs/">PQS</A>).<BR><BR>
|
||
MMDB parses that information to identify the biological unit(s) within the structure record, <A HREF="#DataProcessingBiologicalFormsTypeClassification">compares biological units</A> to each other if two or more are present in order to determine if they are similar or distinct, and uses the results of the parsing and comparison steps to provide a variety of <A HREF="#MmdbsrvDisplayOptions">display options</A> for a structure, such as a concise view showing only the default biological unit, a comprehensive view of all biological units, or the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>. If biological units are displayed, the MMDB summary page indicates the method by which each was determined, as extracted from the "REMARK 350" record of the PDB source file.<BR><BR>
|
||
|
||
MMDB also identifies the non-biopolymers (e.g., chemicals, ions, heme groups, etc.) that are part of the biological unit by analyzing the <A HREF="#DataProcessingInteractions">interactions</A> observed within the structure. If a non-biopolymer has five or more contacts with a biopolymer at an <A HREF="#DataProcessingInteractionsDistanceThreshold">interatomic distance of 4 Å</A> or less, the non-biopolymer is grouped into the relevant biological unit(s).<!-- Å is the HTML code for Angstrom, <20> --> If a non-biopolymer contacts two or more biopolymers, the interaction with the greatest number of contacts takes precedence. <!-- {{In case of a tie...?}} {{The threshold for number of contacts is lower for ions, such as CA+2, in order to ensure that all instances of the ion are considered.}} --> Chemicals that are not biologically significant to the structure, such as crystallization agents, water molecules, detergents, etc. are ignored.<BR><BR>
|
||
|
||
<I>(NOTE: The biological unit display option is not available for <A HREF="#DataProcessingMergeSplitFiles">merged PDB split files</A> from crystallographic studies, because the biological unit of the complete structure is not specified in a computer readable way in the PDB source files. The <A HREF="#SummaryPage">structure summary</A> page for a merged crystallographic structure therefore simply uses the label of "asymmetric unit." In such cases, please refer to the corresponding publication, if/as available, for the author's description of the structure's biologically active form.)</I>
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingBiologicalFormsCrystalSymmetry"></A><A NAME="DataProcessingCrystalSymmetry"></A><B>apply transformations<BR>derived from<BR>crystallographic symmetry</B></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">If the raw data in a structure record represents a portion of the <A HREF="#DataProcessingBiologicalForms">biological unit</A>, <!-- }} -->and if the "REMARK 350" record of the PDB source file specifies the rotational and translational transformations that should be applied to the raw data, MMDB automatically applies these transformations to reconstruct the complete biological unit.<BR><BR>
|
||
|
||
For example, MMDB processing generated the second half of the biological unit for <A HREF="#DataProcessingHumanHemoglobinExamples">human hemoglobin</A> in the <A HREF="#DataProcessingHumanHemoglobinExample2">1LFT</A> structure by applying the transformations specified in the <A HREF="http://www.rcsb.org/pdb/files/1LFT.pdb?headerOnly=YES
|
||
">PDB source file's REMARK 350</A> record. <!-- {{Note: As a result, the <A HREF="#MmdbsrvSave">ASN.1 data file</A> for that record in MMDB contains an additional copy of the alpha and beta protein sequences and the atomic spatial coordinates for each one. The sequence data generated by applying transformations are stored with a local ID (with the format XXX_XX) in the ASN.1 data file for the structure and are <I>not</I> <A HREF="#DataProcessingDeposition">deposited as protein sequence records</A> into the Entrez Protein database. However, they do appear in the Cn3D sequence viewer window.}} --><BR><BR>
|
||
|
||
<I>If any protein or nucleotide molecules in the structure were generated by applying transformations from crystallographic symmetry, they are depicted in the <A HREF="#MmdbsrvThumbnailSchematic">interactions schematic</A> and <A HREF="#MmdbsrvMolecularComponents">molecular components summary table</A> of an <A HREF="#SummaryPage">MMDB summary page</A> with labels that have alphanumeric combinations (for example, <IMG SRC="images/molecular_component_protein_circle_crystal_symmetry.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="Example of circle icons with alphanumeric labels used to depict protein molecules generated by applying transformations from crystallographic symmetry."> or <IMG SRC="images/molecular_component_nucleotide_square_crystal_symmetry.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="Example of square icons with alphanumeric labels used to depict nucleotide sequences generated by applying transformations from crystallographic symmetry.">), indicating the source molecule from which they were generated and the copy number. Chemicals that interact only with such molecules were also generated by applying transformations from crystallographic symmetry.</I>
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingBiologicalFormsTypeClassification"></A><B>compare biological units<BR>within a record to each other<BR>to identify distinct forms</B></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">If multiple <A HREF="#DataProcessingBiologicalForms">biological units</A> exist within a single structure record, or if multiple interpretations of the biological unit have been annotated in the record, MMDB uses an algorithm to compare them to each other and determine if they are the similar or distinct.<BR><BR>
|
||
|
||
Biological units are considered <B>similar</B> if they contain the same number and type of molecular components and meet a threshhold for sequence and structural similarity<!-- (as in the <A HREF="#DataProcessingHumanHemoglobinExample3">1LFL</A> example below) -->. In such a case, they will be assigned the same "type" code on the <!-- only one representative is displayed on the default --> <A HREF="#SummaryPage">MMDB summary page</A> display of "all biological units." The thresholds currently used are 90% or more sequence similarity and an RMSD of 2 Å or less for a global superposition of the biological units.<!-- Å is the HTML code for Angstrom, <20> --> (RMSD is the root mean square superposition residual in Angstroms. This number is calculated after optimal superposition of two structures, as the square root of the mean square distances between equivalent C-alpha atoms. Note that the RMSD value scales with the extent of the structural alignments and that this size must be taken into consideration when using RMSD as a descriptor of overall structural similarity.)<BR><BR>
|
||
|
||
Biological units are considered to be <B>distinct</B> if they do not meet the above threshholds. In that case, each one will be assigned a different "type" code on the <A HREF="#SummaryPage">MMDB summary page</A> display of "all biological units."<!-- each one will appear on the <A HREF="#SummaryPage">MMDB summary page</A> display of <A HREF="#MmdbsrvDisplayOptions">unique biological units</A>, providing a non-redundant view of the biological units that have been detected within the structure record. --><BR><BR>
|
||
|
||
<!-- {{Algorithm details: What are the thresholds for sequence and structural similarity? Are non-biopolymers such as chemicals, ions, heme groups, etc. taken into consideration when comparing the biological units against each other, or does the algorithm look only at the number of biopolymers, their sequence data, and their 3D shape in determining similar vs. distinct biological units within a structure?}}<BR><BR -->
|
||
|
||
For example, if the author has determined that the biological unit of the structure is a tetramer, and a software program has determined it to be a dimer, the interpretations of the biological unit are distinct from each other and <!-- both will be shown --> each one will be assigned a different "type" code on the <A HREF="#SummaryPage">MMDB summary page</A> display of all biological units, along with a corresponding annotation noting how each was determined.<!-- An <A HREF="#MmdbsrvDisplayOptions">option</A> to view the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> is available as well. -->
|
||
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingBiologicalFormsMergeSplitFiles"></A><B>note about biological unit<BR>in merged PDB split files</B></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">Some structures exceed the size limits implicit to the PDB file format and are therefore split into several PDB files. The MMDB data processing procedures <A HREF="#DataProcessingMergeSplitFiles">merge the PDB split files</A> into a single structure record.<BR><BR>
|
||
|
||
The <A HREF="#DataProcessingBiologicalFormsProcedures">biological unit specification</A> is contained in a free text field of the individual <A HREF="#SourceDatabases">PDB source file</A>s. When a structure record has been reconstructed my merging two more PDB split files, that information cannot be parsed in an automated way for the complete structure. Therefore, only the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> is displayed for merged crystallographic structures, representing the unification of raw data from the original PDB files. In the case of structures resolved by <I>electron microscopy (EM)</I> or <I>nuclear magnetic resonance (NMR)</I>, the term "asymmetric unit" does not apply, and the term "biological unit" is shown instead on the summary page for a merged structure from either of those technologies. Please refer to the corresponding publications for those structures, if/as available, for the author's description of their biologically active form.<BR><BR>
|
||
|
||
<!-- The biological unit is generally specified in the REMARK 350 record of an individual PDB source file. However, when a structure record has been reconstructed my merging two more PDB split files, the <A HREF="#DataProcessingBiologicalFormsProcedures">biological unit specification</A> cannot be parsed in an automated way for the complete structure. Therefore, only the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> is displayed, representing the unification of raw data from the original PDB files. Please refer to the corresponding publications for those structures, if/as available, for the author's description of their biologically active form.<BR><BR -->
|
||
|
||
<!-- The biological unit is generally specified in the REMARK 350 record of an individual PDB source file. However, when a structure record has been reconstructed my merging two more PDB split files, the biological unit specification cannot be parsed in an automated way for the complete structure. Therefore, only the asymmetric unit is displayed. -->
|
||
|
||
<!-- If the PDB split files do not contain a REMARK 350 record specifying the <A HREF="#DataProcessingBiologicalForms">biological unit</A>, then {{the biological unit is identified at NCBI using an algorithm that identifies interactions among the component molecules to identify complexes that meet or surpass a threshhold for number of interactions.}}.<BR><BR -->
|
||
|
||
The merged files now make it possible to view and/or download large macromolecular structures in their entirety, and to interactively view the <A HREF="#SequenceStructureRelationship">sequence-structure relationships</A> using the free <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> web-based 3D viewer or the free <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> 4.3 stand-alone software program (<A HREF="../../CN3D/cn3dinstall.shtml">install</A>). You can also <A HREF="/structure?cmd=search&term=2%5BPdbFileCount%5D+%3A+1000%5BPdbFileCount%5D">retrieve all merged files</A>, if desired.
|
||
<!-- A HREF="/structure/99304,99305,99306,99307,99308,99458,99459,99460,99461,99462,99463,99464,99465,99466,99467,99468,99469,99470,99471,99472,99473,99474,99475,99476,99477,99478,99479,99480,99481,99482,99483,99484,99485,99486,99487,99488,99489,99490,99491,99492,99493,99494,99495,99496,99497,99498,99499,99500,99501,99502,99503,99504,99505,99506,99507,99508,99509,99510,99511,99512,99513,99514,99515,99516,99517,99518,99519,99520,99521,99522,99523,99524,99525,99526,99527,99528,99529,99530,99531,99532,99533,99534,99535,99536,99537,99538,99539,99540,99541,99542,99543,99544,99545,99546,99547,99548,99549,99550,99551,99552,99553,99554,99555,99556,99557,99558,99559,99560,99561,99562,99563,99564,99565,99566,99567,99568,99569,99570,99571,99572,99573,99574,99575,99576,99577,99578,99579,99580,99581,99582,99583,99584,99585,99586,99587,99588,99589,99590,99591,99592,99593,99594,99595,99596,99597,99598,99995,99996,99997,99998,100416,100951">retrieve all merged files</A --><BR><BR>
|
||
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- ========= END_DATA_PROCESSING_BIOLOGICAL_FORMS_PROCEDURES =========== -->
|
||
|
||
<!-- ====== ASYMMETRIC_UNIT_TECHNICAL_NOTE ====== -->
|
||
|
||
<A NAME="DataProcessingBiologicalFormsAdditionalNotes"></A>
|
||
<A NAME="DataProcessingAsymmetricUnit"></A>
|
||
<A NAME="AsymmetricUnit"></A>
|
||
|
||
<P class="indent20 NormalText"><B>Asymmetric unit (technical note):<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></B></P>
|
||
<BR>
|
||
|
||
<P class="indent20 NormalText">
|
||
<!-- B>Asymmetric Unit:</B -->The <B>raw data</B> in a structure record (generated by <A HREF="#DataTypeExperimentalMethods">x-ray crystallography</A> or neutron diffraction) are often casually referred to as the "<B>asymmetric unit</B>." These data, which were <B>submitted by the author</B> and stored in the <A HREF="#SourceDatabases">source PDB record</A>, <B>can represent either</B>: <B>(a)</B> the complete <A HREF="#DataProcessingBiologicalForms">biological unit</A> (i.e, the biochemically active form of a biomolecule); <B>(b)</B> a portion of the biological unit; or <B>(c)</B> multiple copies of the biological unit, as shown in the illustrated example of three different <A HREF="#DataProcessingHumanHemoglobinExamples">human hemoglobin</A> structure records. The <A HREF="#MmdbsrvDisplayOptions">display options</A> on an <A HREF="#SummaryPage">MMDB summary page</A> for an individual structure allow you to view your choice of biological unit(s) or asymmetric unit, with the biological unit shown by default.<BR><BR>
|
||
|
||
The "asymmetric unit" is equivalent to the <A HREF="#DataProcessingBiologicalForms">biological unit</A> in approximately 60% of structure records<!-- as of May 2011 -->.<!-- [(as in the <A HREF="#DataProcessingHumanHemoglobinExamples">human hemoglobin</A> example <A HREF="#DataProcessingHumanHemoglobinExample1">2DN2</A>).] In those cases, the <A HREF="#SummaryPage">MMDB summary page</A> will still provide access to both views, with the biological unit displayed by default. [If you choose to display the asymmetric unit, a note will appear beside its molecular graphic, indicating that the asymmetric unit it is equivalent to the biological unit. If you choose to display the biological unit, an <A HREF="#MmdbsrvThumbnailSchematic">interaction schematic</A> will be displayed beside its <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A>.][An interaction schematic is displayed only in the view of the biological unit.] --><BR><BR>
|
||
|
||
The concepts of asymmetric unit and <A HREF="#DataProcessingBiologicalForms">biological unit</A> do not apply to structure records resolved by <A HREF="#DataTypeExperimentalMethods">experimental methods</A> other than x-ray crystallography and neutron diffraction.<BR><BR>
|
||
|
||
<I>Note: The <B>technical definition</B> of asymmetric unit is somewhat different from its casual meaning. Technically, an asymmetric unit is the smallest part of a 3D structure from which the complete structure can be built using a specific set of rotational and translational matrices that describe the symmetry of the structure.</I>
|
||
|
||
<!-- The biological unit of some proteins is a monomer rather than an assembly of multiple protein molecules.<BR><BR -->
|
||
|
||
<!-- In approximately 60% of structure records (as of May 2011), the asymmetric unit is equivalent to the biological unit. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>, or it represents multiple copies of the biological unit. -->
|
||
|
||
<!-- A NAME="DataProcessingBiologicalFormVsAsymmetricUnit"></A>
|
||
<B>MMDB display of Biologial Unit vs. Asymmetric Unit:</B> By default, the <A HREF="#SummaryPage">MMDB summary page</A> for a structure displays a <A HREF="#MmdbsrvThumbnailImageDisplayOptions">thumbnail image</A> of each <A HREF="#DataProcessingBiologicalFormsTypeClassification">unique biological unit</A> found within the record, thereby providing a non-redundant view of the biochemical units within the structure. {{The summary page also provides an option to view all biological units, if two or more have been identified, or the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>.}} -->
|
||
|
||
</P>
|
||
<BR>
|
||
|
||
<!-- ====== END_ASYMMETRIC_UNIT_TECHNICAL_NOTE ====== -->
|
||
|
||
<!-- ====== DATA_PROCESSING_MERGE_SPLIT_FILES_EXAMPLES ====== -->
|
||
|
||
<A NAME="DataProcessingMergeSplitFiles"></A>
|
||
<A NAME="MergePDBSplitFiles"></A>
|
||
<A NAME="MergeSplitFiles"></A>
|
||
<A NAME="PDBSplitFiles"></A>
|
||
<P class="MiniText"> </P>
|
||
|
||
<P><B>Merging PDB split files into a single MMDB structure record</B><img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
Some structures exceed the size limits implicit to the PDB file format and are therefore split into several PDB files. The MMDB data processing procedures merge the PDB split files into a single structure record. The merged structures now make it possible to <B>display and/or download large macromolecular structures</B> in their entirety, and to <B>interactively view the</B> <A HREF="#SequenceStructureRelationship"><B>sequence-structure relationships</B></A> using either <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A>, a web-based 3D viewer that loads the structure within the web page without the need to install a separate application, or the stand-alone <A HREF="../../CN3D/cn3d.shtml"><B>Cn3D</B></A> 4.3 (<A HREF="../../CN3D/cn3dinstall.shtml">install</A>).<BR><BR>
|
||
|
||
Please note that "<A HREF="#AsymmetricUnit"><B>asymmetric unit</B></A>" is the only <A HREF="#MmdbsrvDisplayOptions">display option</A> for <A HREF="#DataProcessingMergeSplitFiles">merged PDB split files</A> from <I>crystallographic studies</I>, because the <A HREF="#DataProcessingBiologicalForms"><B>biological unit</B></A> of the complete structure is not specified in a computer readable way in the PDB source files. The <A HREF="#SummaryPage">structure summary</A> page for a merged crystallographic structure therefore simply uses the label of "<!-- A HREF="#DataProcessingAsymmetricUnit" -->asymmetric unit" above the molecular graphic, because it represents the unification of raw data from the original PDB files. The asymmetric unit can represent the structure's complete biological unit, a portion of the biological unit, or multiple copies of the biological unit. In the case of structures resolved by <I>electron microscopy (EM)</I> or <I>nuclear magnetic resonance (NMR)</I>, the term "asymmetric unit" does not apply, and the term "biological unit" is shown instead on the summary page for a merged structure from either of those technologies. Please refer to the corresponding publication for a structure, if/as available, for the author's description of its biologically active form.<BR><BR>
|
||
|
||
<!-- ALT WORDING: Please note that the <A HREF="#SummaryPage">summary page</A> for a merged structure displays only the <A HREF="#AsymmetricUnit">asymmetric unit</A> (raw crystallographic data) of the structure, because the <A HREF="#DataProcessingBiologicalForms">biological unit</A> of the complete structure is not specified in a computer readable way in the PDB source files. The asymmetric unit can represent the structure's complete biological unit, a portion of the biological unit, or multiple copies of the biological unit. Please refer to the corresponding publication for a structure, if/as available, for the author's description of its biologically active form.<BR><BR -->
|
||
|
||
Examples of merged structures, illustrated below, include the:</P>
|
||
|
||
<UL>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_1VU0_ViralCapsidAav6"><!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=99554" --><B>viral capsid</B></A> by Xie et al.</LI>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault"><!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=99596" --><B>rat liver vault</B></A> by Tanaka et al.</LI>
|
||
<LI><A HREF="#DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel"><!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=99580" --><B>ribosome structure</B></A> by <A HREF="http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2009/">Nobel Laureate V. Ramakrishnan</A></LI>
|
||
</UL>
|
||
|
||
<P class="indent20">
|
||
You can also <A HREF="/structure?cmd=search&term=2%5BPdbFileCount%5D+%3A+1000%5BPdbFileCount%5D"><B>retrieve all merged files</B></A> from the Molecular Modeling Database, if desired.
|
||
<!-- A HREF="/structure/99304,99305,99306,99307,99308,99458,99459,99460,99461,99462,99463,99464,99465,99466,99467,99468,99469,99470,99471,99472,99473,99474,99475,99476,99477,99478,99479,99480,99481,99482,99483,99484,99485,99486,99487,99488,99489,99490,99491,99492,99493,99494,99495,99496,99497,99498,99499,99500,99501,99502,99503,99504,99505,99506,99507,99508,99509,99510,99511,99512,99513,99514,99515,99516,99517,99518,99519,99520,99521,99522,99523,99524,99525,99526,99527,99528,99529,99530,99531,99532,99533,99534,99535,99536,99537,99538,99539,99540,99541,99542,99543,99544,99545,99546,99547,99548,99549,99550,99551,99552,99553,99554,99555,99556,99557,99558,99559,99560,99561,99562,99563,99564,99565,99566,99567,99568,99569,99570,99571,99572,99573,99574,99575,99576,99577,99578,99579,99580,99581,99582,99583,99584,99585,99586,99587,99588,99589,99590,99591,99592,99593,99594,99595,99596,99597,99598,99995,99996,99997,99998,100416,100951">retrieve all merged files</A -->
|
||
<!-- Please refer to the corresponding publications for those structures, if/as available, for the author's description of their biologically active form. -->
|
||
</P>
|
||
<BR><BR>
|
||
|
||
|
||
<!-- ====== DATA_PROCESSING_MERGE_SPLIT_FILES_VIRAL_CAPSID_Aav6_EXAMPLE ====== -->
|
||
|
||
<A NAME="DataProcessingMergeSplitFilesExample_1VU0_ViralCapsidAav6"></A>
|
||
<A NAME="PDBSplitFileViralCapsid"></A>
|
||
<P class="indent20">
|
||
<SPAN style="background-color: #FFFF00"><B>Example:</B> The <B>viral capsid</B></SPAN> for the Adeno-associated Virus Serotype 6 (Aav-6) by <A HREF="/pubmed/21917284">Xie et al.</A> was split into PDB records <!-- A HREF="/structure/93977" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=1VU0" -->1VU0<!-- /A -->, <!-- A HREF="/structure/93978" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=1VU1" -->1VU1<!-- /A -->, <!-- A HREF="/structure/94103" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=3TSX" -->3TSX<!-- /A -->, and was merged at MMDB into a single record with the MMDB ID <A HREF="/structure/99554"><B>99554</B></A>:
|
||
<!-- B>Click</B> on the thumbnail image of the merged file, below, to open it interactively in stand-alone <A HREF="../../CN3D/cn3d.shtml"><B>Cn3D</B></A> 4.3. (If you do not yet have Cn3D 4.3 on your computer, <A HREF="../../CN3D/cn3dinstall.shtml">install</A> it before clicking the thumbnail.) Alternatively, <B>open</B> the <A HREF="/structure/99554"><b>structure summary page for MMDB ID 99554</b></A> in the Molecular Modeling Database, then click on the "<b>3D view</b>" or the "<b>full-featured 3D viewer</b>" button near the bottom of the <A HREF="#MmdbsrvThumbnailMolecularGraphic"><b>molecular graphic</b></A> to interactively view the structure with <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A>, a web-based 3D viewer that loads the structure within the web page without the need to install a separate application. -->
|
||
</P>
|
||
<BR>
|
||
|
||
<A NAME="PDBSplitFileViralCapsidIllustration"></A>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="0">
|
||
<TR>
|
||
<TD width="20"> </TD>
|
||
<TD>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" WIDTH="700" border="0" class="format1 TableText1">
|
||
|
||
<TR>
|
||
|
||
<TD valign="top" align="center" class="format1H" colspan="3"><!-- A HREF="/sites/entrez?cmd=search&db=structure&term=1VU0[accn]+OR+1VU1[accn]+OR+3TSX[accn]" -->PDB SPLIT FILES<!-- /A --> for the <!-- viral capsid: -->Adeno-associated Virus Serotype 6 (Aav-6)</TD>
|
||
|
||
<TD valign="center" align="center" width="14" class="format1H"><IMG SRC="../../IMG/arrow_red_right1.png" WIDTH="12" HEIGHT="20" BORDER="0" ALT="right arrow"></TD>
|
||
|
||
<TD valign="top" align="center" class="format1H">MMDB MERGED FILE</TD>
|
||
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_1VU0_ViralCapsidAav6_split1"></A>PDB ID: <!-- A HREF="/structure/93977" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=1VU0" --><B>1VU0</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/93977"><B>93977</B></A --></TD>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_1VU0_ViralCapsidAav6_split2"></A>PDB ID: <!-- A HREF="/structure/93978" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=1VU1" --><B>1VU1</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/93978"><B>93978</B></A --></TD>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_1VU0_ViralCapsidAav6_split3"></A>PDB ID: <!-- A HREF="/structure/94103" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=3TSX" --><B>3TSX</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/94103"><B>94103</B></A --></TD>
|
||
|
||
<TD valign="center" align="center" width="12" class="format1H"><IMG SRC="../../IMG/arrow_red_right1.png" WIDTH="12" HEIGHT="20" BORDER="0" ALT="right arrow"></TD>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_1VU0_ViralCapsidAav6_merged"></A>MMDB ID: <A HREF="/structure/99554"><B>99554</B></A></TD>
|
||
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/viral_capsid_Aav6_split1_1VU0_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="First of three PDB split files for the viral capsid Aav-6, showing the 3D view for the portion of the structure that is in PDB record 1VU0."></TD>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/viral_capsid_Aav6_split2_1VU1_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="Second of three PDB split files for the viral capsid Aav-6, showing the 3D view for the portion of the structure that is in PDB record 1VU1"></TD>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/viral_capsid_Aav6_split3_3TSX_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="Last of three PDB split files for the viral capsid Aav-6, showing the 3D view for the portion of the structure that is in PDB record 3TSX."></TD>
|
||
|
||
<TD valign="top" align="center" width="12" class="format1H"><IMG SRC="../../IMG/arrow_red_right1.png" WIDTH="12" HEIGHT="20" BORDER="0" ALT="right arrow"></TD>
|
||
|
||
<TD valign="top" class="format1B"><A HREF="data/viral_capsid_Aav6_merged_mmdbid99554.cn3"><IMG SRC="images/viral_capsid_Aav6_merged_mmdbid99554_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="Thumbnail image of the Adeno-associated Virus Serotype 6 (Aav-6), in which the data from the three PDB split files have been merged together to provide a 3D view of the complete structure, shown here in MMDB ID 99554. The entire structure and its sequence data can be viewed interactively with the free stand-alone Cn3D program, or with the free web-based iCn3D program."></A><BR>Click on the thumbnail image above to open the merged file in the free stand-alone <A HREF="../../CN3D/cn3d.shtml"><b>Cn3D</b></A> 4.3 viewer to interactively view the entire structure and its sequence data. (If you do not yet have Cn3D 4.3 on your computer, <A HREF="../../CN3D/cn3dinstall.shtml">install</A> it before clicking the thumbnail.)<BR><BR>
|
||
Alternatively, open the <A HREF="/structure/99554">structure summary page for MMDB ID 99554</A> in the Molecular Modeling Database, then click on the "full-featured 3D viewer" button <!-- IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_icon_spin_structure.png" width="22" height="19" border="0" --> near the bottom of the <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A> to <A HREF="/Structure/icn3d/full.html?&mmdbid=99554&bu=1&showanno=1"><B>interactively view the structure of the viral capsid with iCn3D</B></A>, a <b>web-based 3D viewer</b> that loads the structure within the web page without the need to install a separate application.
|
||
</TD>
|
||
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR><BR>
|
||
<!-- ====== END_DATA_PROCESSING_MERGE_SPLIT_FILES_VIRAL_CAPSID_EXAMPLE ====== -->
|
||
|
||
|
||
<!-- ====== DATA_PROCESSING_MERGE_SPLIT_FILES_RAT_LIVER_VAULT_EXAMPLE ====== -->
|
||
|
||
<A NAME="DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault"></A>
|
||
<A NAME="PDBSplitFileRatLiverVault"></A>
|
||
<P class="indent20">
|
||
<SPAN style="background-color: #FFFF00"><B>Example:</B> The <B>rat liver vault</B></SPAN> by <A HREF="/pubmed/19150846">Tanaka et al.</A> was split into PDB records <!-- A HREF="/structure/68966" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2ZUO" -->2ZUO<!-- /A -->, <!-- A HREF="/structure/68967" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2ZV4" -->2ZV4<!-- /A -->, <!-- A HREF="/structure/68968" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2ZV5" -->2ZV5<!-- /A -->, and was merged at MMDB into a single record with the MMDB ID <A HREF="/structure/99596"><B>99596</B></A>:
|
||
<!-- B>Click</B> on the thumbnail image of the merged file, below, to open it interactively in stand-alone <A HREF="../../CN3D/cn3d.shtml"><B>Cn3D</B></A> 4.3. (If you do not yet have Cn3D 4.3 on your computer, <A HREF="../../CN3D/cn3dinstall.shtml">install</A> it before clicking the thumbnail.) Alternatively, <B>open</B> the <A HREF="/structure/99554"><b>structure summary page for MMDB ID 99554</b></A> in the Molecular Modeling Database, then click on the "<b>3D view</b>" or the "<b>full-featured 3D viewer</b>" button near the bottom of the <A HREF="#MmdbsrvThumbnailMolecularGraphic"><b>molecular graphic</b></A> to interactively view the structure with <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A>, a web-based 3D viewer that loads the structure within the web page without the need to install a separate application. -->
|
||
<BR>
|
||
<I>(Note: The merged file represents half of the <A HREF="#DataProcessingBiologicalForms">biological unit</A>, as it was submitted by the author. The <A HREF="#DataProcessingBiologicalFormsProcedures">procedures to identify biological units</A> cannot be applied in an automated way to a merged file<!--, as the biological unit specification is stored in a free text field of the individual PDB source files. -->; therefore, the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> is diplayed instead. Please refer to the corresponding publication for a structure for the author's description of the biologically active form.
|
||
<!-- The specifications for applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A> to construct the complete biological unit are contained in the REMARK 350 record of the individual PDB source files. However, when a structure record has been reconstructed my merging two more PDB split files, the biological unit specifications cannot be parsed in an automated way for the complete structure. Therefore, only the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> is displayed. -->
|
||
<!-- However, they exist as free text and therefore cannot be applied in an automated way during the MMDB data processing <A HREF="#DataProcessingBiologicalFormsProcedures">procedures</A> for identifying and displaying biological units in the merged structures. -->)</I>
|
||
</P>
|
||
<BR>
|
||
|
||
<A NAME="PDBSplitFileRatLiverVaultIllustration"></A>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="0">
|
||
<TR>
|
||
<TD width="20"> </TD>
|
||
<TD>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" WIDTH="700" border="0" class="format1 TableText1">
|
||
|
||
<TR>
|
||
|
||
<TD valign="top" align="center" class="format1H" colspan="3"><!-- A HREF="/sites/entrez?cmd=search&db=structure&term=2ZUO[accn]+OR+2ZV5[accn]+OR+2ZV4[accn]" -->PDB SPLIT FILES<!-- /A --> for the Rat Liver Vault</TD>
|
||
|
||
<TD valign="center" align="center" width="14" class="format1H"><IMG SRC="../../IMG/arrow_red_right1.png" WIDTH="12" HEIGHT="20" BORDER="0" ALT="right arrow"></TD>
|
||
|
||
<TD valign="top" align="center" class="format1H">MMDB MERGED FILE</TD>
|
||
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault_split1"></A>PDB ID: <!-- A HREF="/structure/68966" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2ZUO" --><B>2ZUO</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/68966"><B>68966</B></A --></TD>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault_split2"></A>PDB ID: <!-- A HREF="/structure/68967" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2ZV4" --><B>2ZV4</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/68967"><B>68967</B></A --></TD>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault_split3"></A>PDB ID: <!-- A HREF="/structure/68968" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2ZV5" --><B>2ZV5</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/68968"><B>68968</B></A --></TD>
|
||
|
||
<TD valign="center" align="center" width="12" class="format1H"><IMG SRC="../../IMG/arrow_red_right1.png" WIDTH="12" HEIGHT="20" BORDER="0" ALT="right arrow"></TD>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault_merged"></A>MMDB ID: <A HREF="/structure/99596"><B>99596</B></A></TD>
|
||
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/rat_liver_vault_split1_2ZUO_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="First of three PDB split files for the rat liver vault, showing the 3D view for the portion of the structure that is in PDB record 2ZUO."></TD>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/rat_liver_vault_split2_2ZV4_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="Second of three PDB split files for the rat liver vault, showing the 3D view for the portion of the structure that is in PDB record 2ZV4"></TD>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/rat_liver_vault_split3_2ZV5_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="Last of three PDB split files for the rat liver vault, showing the 3D view for the portion of the structure that is in PDB record 2ZV5."></TD>
|
||
|
||
<TD valign="top" align="center" width="12" class="format1H"><IMG SRC="../../IMG/arrow_red_right1.png" WIDTH="12" HEIGHT="20" BORDER="0" ALT="right arrow"></TD>
|
||
|
||
<TD valign="top" class="format1B"><A HREF="data/rat_liver_vault_merged_mmdbid99596.cn3"><IMG SRC="images/rat_liver_vault_merged_mmdbid99596_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="Thumbnail image of the rat liver vault, in which the data from the three PDB split files have been merged together to provide a 3D view of the complete data set, shown here in MMDB ID 99596."></A><BR>
|
||
Click on the thumbnail image above to open the merged file in the stand-alone <A HREF="../../CN3D/cn3d.shtml"><b>Cn3D</b></A> 4.3 viewer to interactively view the entire structure and its sequence data. (If you do not yet have Cn3D 4.3 on your computer, <A HREF="../../CN3D/cn3dinstall.shtml">install</A> it before clicking the thumbnail.)<BR><BR>
|
||
Alternatively, open the <A HREF="/structure/99596">structure summary page for MMDB ID 99596</A> in the Molecular Modeling Database, then click on the "3D view" or the "full-featured 3D viewer" button near the bottom of the <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A> to <A HREF="/Structure/icn3d/full.html?&mmdbid=99596&bu=1&showanno=1"><B>interactively view the rat liver vault structure with iCn3D</B></A>, a <b>web-based 3D viewer</b> that loads the structure within the web page without the need to install a separate application.</TD>
|
||
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR><BR>
|
||
<!-- ====== END_DATA_PROCESSING_MERGE_SPLIT_FILES_RAT_LIVER_VAULT_EXAMPLE ====== -->
|
||
|
||
|
||
<!-- ====== DATA_PROCESSING_MERGE_SPLIT_FILES_RIBOSOME_EXAMPLE_Ramakrishnan ====== -->
|
||
|
||
<A NAME="DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel"></A>
|
||
<A NAME="PDBSplitFileRibosome"></A>
|
||
<P class="indent20">
|
||
<SPAN style="background-color: #FFFF00"><B>Example:</B> The <B>ribosome</B></SPAN> structure by <A HREF="/pubmed/16959973">Selmer, Dunham, Murphy, Weixlbaumer, Petry, Kelley, Weir, and Ramakrishnan</A>, the <A HREF="http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2009/">2009 Nobel Laureate in Chemistry</A>, was split into PDB records <!-- A HREF="/structure/84967" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2XFZ" -->2XFZ<!-- /A -->, <!-- A HREF="/structure/84968" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2XG0" -->2XG0<!-- /A -->, <!-- A HREF="/structure/84969" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2XG1" -->2XG1<!-- /A -->, <!-- A HREF="/structure/84970" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2XG2" -->2XG2<!-- /A -->, and was merged at MMDB into a single record with the MMDB ID <A HREF="/structure/99580"><B>99580</B></A>:
|
||
<!-- B>Click</B> on the thumbnail image of the merged file, below, to open it interactively in stand-alone <A HREF="../../CN3D/cn3d.shtml"><B>Cn3D</B></A> 4.3. (If you do not yet have Cn3D 4.3 on your computer, <A HREF="../../CN3D/cn3dinstall.shtml">install</A> it before clicking the thumbnail.) Alternatively, <B>open</B> the <A HREF="/structure/99554"><b>structure summary page for MMDB ID 99554</b></A> in the Molecular Modeling Database, then click on the "<b>3D view</b>" or the "<b>full-featured 3D viewer</b>" button near the bottom of the <A HREF="#MmdbsrvThumbnailMolecularGraphic"><b>molecular graphic</b></A> to interactively view the structure with <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A>, a web-based 3D viewer that loads the structure within the web page without the need to install a separate application. --><BR>
|
||
<I>(Note: The merged file represents two copies of the <A HREF="#DataProcessingBiologicalForms">biological unit</A>, as submitted by the author. The <A HREF="#DataProcessingBiologicalFormsProcedures">procedures to identify biological units</A> cannot be applied in an automated way to a merged file<!--, as the biological unit specification is stored in a free text field of the individual PDB source files. -->; therefore, the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> is diplayed instead. Please refer to the corresponding publication for a structure for the author's description of the biologically active form.
|
||
<!-- The biological unit is generally specified in the REMARK 350 record of an individual PDB source file. However, when a structure record has been reconstructed my merging two more PDB split files, the <A HREF="#DataProcessingBiologicalFormsProcedures">biological unit specification</A> cannot be parsed in an automated way for the complete structure. Therefore, only the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> is displayed. -->)</I>
|
||
</P>
|
||
<BR>
|
||
|
||
<A NAME="PDBSplitFileRibosomeIllustration"></A>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="0">
|
||
<TR>
|
||
<TD width="20"> </TD>
|
||
<TD>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" WIDTH="700" border="0" class="format1 TableText1">
|
||
|
||
<TR>
|
||
|
||
<TD valign="top" align="center" class="format1H" colspan="4"><!-- A HREF="/sites/entrez?cmd=search&db=structure&term=2XFZ[accn]+OR+2XG0[accn]+OR+2XG1[accn]+OR+2XG2[accn]" -->PDB SPLIT FILES<!-- /A --> for the Structure of Cytotoxic Domain of Colicin E3 Bound to the 70S Ribosome</TD>
|
||
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel_split1"></A>PDB ID: <!-- A HREF="/structure/84967" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2XFZ" --><B>2XFZ</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/84967"><B>84967</B></A --></TD>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel_split2"></A>PDB ID: <!-- A HREF="/structure/84968" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2XG0" --><B>2XG0</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/84968"><B>84968</B></A --></TD>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel_split3"></A>PDB ID: <!-- A HREF="/structure/84969" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2XG1" --><B>2XG1</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/84969"><B>84969</B></A --></TD>
|
||
|
||
<TD valign="center" class="format1A"><A NAME="DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel_split4"></A>PDB ID: <!-- A HREF="/structure/84970" --><!-- A HREF="http://www.rcsb.org/pdb/explore/explore.do?structureId=2XG2" --><B>2XG2</B><!-- /A -->
|
||
<!-- BR>MMDB ID: <A HREF="/structure/84970"><B>84970</B></A --></TD>
|
||
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/ribosome_nobel_split1_2XFZ_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="First of four PDB split files for the ribosome structure by Nobel Laureate Ramakrishnan, showing the 3D view for the portion of the structure that is in PDB record 2XFZ."></TD>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/ribosome_nobel_split2_2XG0_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="Second of four PDB split files for the ribosome structure by Nobel Laureate Ramakrishnan, showing the 3D view for the portion of the structure that is in PDB record 2XG0"></TD>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/ribosome_nobel_split3_2XG1_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="Third of four PDB split files for the ribosome structure by Nobel Laureate Ramakrishnan, showing the 3D view for the portion of the structure that is in PDB record 2XG1."></TD>
|
||
|
||
<TD valign="top" class="format1B"><IMG SRC="images/ribosome_nobel_split4_2XG2_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="Last of four PDB split files for the ribosome structure by Nobel Laureate Ramakrishnan, showing the 3D view for the portion of the structure that is in PDB record 2XG2."></TD>
|
||
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
<TD valign="center" align="center" class="format1H" rowspan="1" colspan="4">
|
||
<IMG SRC="../../IMG/arrow_red_down1.png" WIDTH="22" HEIGHT="13" BORDER="0" ALT="right arrow"><BR>
|
||
MMDB MERGED FILE: Complete structure of the Structure of Cytotoxic Domain of Colicin E3 Bound to the 70S Ribosome<BR>
|
||
<A NAME="DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel_merged"></A>MMDB ID: <A HREF="/structure/99580"><B>99580</B></A></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" align="center" class="format1B" colspan="4">
|
||
|
||
<!-- A HREF="/structure/99580" --><IMG SRC="images/ribosome_nobel_interactions_schematic_mmdbid99580_thumbnail_no_header_bar.png" WIDTH="150" HEIGHT="150" BORDER="0" ALT="Interactions schematic for the ribosome structure by Nobel Laureate Ramakrishnan, showing the interactions among the component molecules, and indicating that two copies of the ribosome are present in the structure file."><!-- /A -->
|
||
<!-- {NOTE: links to the structure summary page for MMDB ID 99580 were commented out on 9/23/2016 because that page times out for some reason; once the summary page is loading properly again, un-comment out the links to it and add this sentence to the end of the "ALT" text: Click on the graphic to open the structure summary page for MMDB ID 99580, from which the interaction schematic was taken.} -->
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0">
|
||
|
||
<A HREF="data/ribosome_nobel_merged_mmdbid99580.cn3"><IMG SRC="images/ribosome_nobel_merged_mmdbid99580_thumbnail_no_header_bar.png" WIDTH="163" HEIGHT="150" BORDER="0" ALT="The MMDB record for the complete ribosome structure by Nobel Laureate Ramakrishnan, in which the data from four PDB split files have been merged together to provide a 3D view of the complete structure, shown here in MMDB ID 99580. Click on the image to open the merged file in Cn3D and interactively view the entire structure and its sequence data."></A><BR><BR>
|
||
|
||
Click on the thumbnail image above to open the merged file in the stand-alone <A HREF="../../CN3D/cn3d.shtml"><b>Cn3D</b></A> 4.3 viewer to interactively view the entire structure and its sequence data. (If you do not yet have Cn3D 4.3 on your computer, <A HREF="../../CN3D/cn3dinstall.shtml">install</A> it before clicking the thumbnail.)<BR><BR>
|
||
Alternatively, open the <A HREF="/structure/99580">structure summary page for MMDB ID 99580</A> in the Molecular Modeling Database, then click on the "3D view" or the "full-featured 3D viewer" button near the bottom of the <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A> to <A HREF="/Structure/icn3d/full.html?&mmdbid=99580&bu=1&showanno=1"><B>interactively view the ribosome structure with iCn3D</B></A>, a <b>web-based 3D viewer</b> that loads the structure within the web page without the need to install a separate application.<BR><BR>
|
||
<I>Note: the <A HREF="#MmdbsrvThumbnailSchematic">interactions schematic</A>, shown above and also visible on the structure summary page for MMDB ID: <A HREF="/structure/99580">99580</A>, indicates that there are two copies of the ribosome in the structure file, reflecting the data submitted by the author.</I><BR><BR></TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ==== END_DATA_PROCESSING_MERGE_SPLIT_FILES_RIBOSOME_EXAMPLE_Ramakrishnan ==== -->
|
||
|
||
</P>
|
||
<BR><BR>
|
||
|
||
<P class="indent20 NormalText">
|
||
In summary, the merged structure files, such as the <A HREF="#DataProcessingMergeSplitFilesExample_1VU0_ViralCapsidAav6"><!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=99554" -->viral capsid </A><!-- by Xie et al., -->, the <A HREF="#DataProcessingMergeSplitFilesExample_2ZUO_RatLiverVault"><!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=99596" -->rat liver vault</A><!-- by Tanaka et al., -->, and the <A HREF="#DataProcessingMergeSplitFilesExample_2XFZ_RibosomeNobel"><!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=99580" -->ribosome</A> illustrated above, now make it possible to view and/or download large macromolecular structures in their entirety, and to interactively view the <A HREF="#SequenceStructureRelationship">sequence-structure relationships</A> using the free stand-alone <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> 4.3 program (<A HREF="../../CN3D/cn3dinstall.shtml">install</A>), or the free web-based <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A> viewer. You can also <A HREF="/sites/entrez?db=structure&Cmd=search&term=2%5BPdbFileCount%5D+%3A+1000%5BPdbFileCount%5D"><B>retrieve all merged files</B></A> from the Molecular Modeling Database, if desired.
|
||
<!-- A HREF="/structure/99304,99305,99306,99307,99308,99458,99459,99460,99461,99462,99463,99464,99465,99466,99467,99468,99469,99470,99471,99472,99473,99474,99475,99476,99477,99478,99479,99480,99481,99482,99483,99484,99485,99486,99487,99488,99489,99490,99491,99492,99493,99494,99495,99496,99497,99498,99499,99500,99501,99502,99503,99504,99505,99506,99507,99508,99509,99510,99511,99512,99513,99514,99515,99516,99517,99518,99519,99520,99521,99522,99523,99524,99525,99526,99527,99528,99529,99530,99531,99532,99533,99534,99535,99536,99537,99538,99539,99540,99541,99542,99543,99544,99545,99546,99547,99548,99549,99550,99551,99552,99553,99554,99555,99556,99557,99558,99559,99560,99561,99562,99563,99564,99565,99566,99567,99568,99569,99570,99571,99572,99573,99574,99575,99576,99577,99578,99579,99580,99581,99582,99583,99584,99585,99586,99587,99588,99589,99590,99591,99592,99593,99594,99595,99596,99597,99598,99995,99996,99997,99998,100416,100951">retrieve all merged files</A -->
|
||
|
||
Please refer to the corresponding publications for those structures, if/as available, for the author's description of their biologically active form.
|
||
|
||
<!-- I>(NOTE: The <A HREF="#SummaryPage">structure summary</A> page for a merged crystallographic structure simply uses the label of "<A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>" above the molecular graphic, as it represents the unification of raw data from the original PDB files. The asymmetric unit might represent the biological unit, multiple copies of the biological unit, or in the case of the rat liver vault, a partial biological unit that can be reconstructed into a complete biological unit by applying transformations from crystallographic symmetry. Because the <A HREF="#DataProcessingBiologicalForms">biological unit</A> of the complete structure is not specified in a computer readable way in the PDB source files, it is not provided as a <A HREF="#MmdbsrvDisplayOptions">display option</A> for a merged crystallographic structure. Therefore, please refer to the corresponding publication for a structure, if/as available, for the author's description of its biologically active form.)</I --><BR><BR><BR>
|
||
</P>
|
||
|
||
<!-- ====== END_DATA_PROCESSING_MERGE_SPLIT_FILES_EXAMPLES ====== -->
|
||
|
||
|
||
<!-- ============ DATA_PROCESSING_INTERACTIONS ============ -->
|
||
|
||
<A NAME="DataProcessingInteractions"></A>
|
||
<P><B>Identify interactions among molecular components</B>:<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
</BR>
|
||
|
||
<P class="indent20">As part of MMDB <A HREF="#DataProcessing">data processing</A>, the spatial coordinates in a structure record are analyzed to identify interactions among the structure's <A HREF="#MmdbsrvMolecularComponents">molecular components</A>. Interactions are reported on an <A HREF="#SummaryPage">MMDB Summary Page</A> as an <A HREF="#MmdbsrvThumbnailSchematic">interactions schematic</A><!-- (and in the table of <A HREF="#MmdbsrvMolecularComponents">molecules and interactions</A>) --> if they meet the following thresholds:</P>
|
||
|
||
<P class="indent20 MiniText"> </P>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingInteractionsDistanceThreshold"></A><B>4 Å interatomic distance</B><!-- Å is the HTML code for Angstrom, <20> --></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">A contact is defined as a distance of 4 Å or less between the heavy atoms of biopolymers (proteins, DNA, and/or RNA).<!-- Å is the HTML code for Angstrom, <20> --> Interactions are identified in a pairwise fashion. For examples, if protein molecules A, B, and C form a trimer, the interactions will be reported between each pair of proteins (e.g., A:B, B:C, and A:C).<BR>
|
||
Interactions between the heavy atoms of biopolymers and chemicals are also reported. <!-- Interactions between chemicals only are not computed. -->
|
||
<!-- {{Aron, 2/3/2011 -- There are a few structures with no biopolymers -- Do they have a biological unit noted in the REMARK 350 record? Note: If a certain fraction of residues are non-standard, MMDB regards them as non-biopolymers (i.e., they are not classified as protein/polypeptide, DNA or RNA). For example, circular peptides have biopolymer properties but are not biopolymers in the classical sense.}} -->
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingInteractionsContactNumberThreshold"></A><B><!-- >= -->5 or more contacts</B></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">
|
||
An interaction between two molecular components is reported on a structure's <A HREF="#SummaryPage">summary page</A> if five or more contacts exist between those molecules<!-- , and if at least one of those molecules is a biopolymer (i.e., protein, DNA, or RNA) -->.
|
||
For example, atoms from at least 5 amino acids or nucleotides in a biopolymer (protein, DNA, or RNA) must be closer than, or as close as, 4 Angstroms from one or more atoms in the "other molecule" in order for the interaction to be reported.
|
||
<!-- Specifically, atoms from at least 5 amino acids or nucleotides in the biopolymer must be ≤ 4 Angstroms to one or more atoms in "the other molecule." -->
|
||
<!-- For example, if atoms from at least 5 amino acids or nucleotides in biopolymer X are ≤ 4 Angstroms to one or more atoms in the other molecule, "Y," a line between those two molecules is drawn in the <A HREF="#MmdbsrvThumbnailSchematic">interaction schematic</A>. If Y is a chemical, a reciprocal interaction is automatically listed in the table of molecules and interactions. If Y is a biopolymer, a reciprocal interaction is listed in the table of molecules and interactions only if 5 or more amino acids f rom Y are in contact with X.-->
|
||
<!-- An interaction between two molecular components is reported on a structure's <A HREF="#SummaryPage">summary page</A> if five or more contacts exist between those molecules. Note that a single atom in one molecule can contact 5 or more atoms in another molecule. Such an interaction will be reported because it meets the threshold of 5 or more contacts. --></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingInteractionsRank"></A><B>rank interactions</B></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">Interactions among the <A HREF="#MmdbsrvMolecularComponents">molecular components</A> are ranked by the number of contacts that meet the 4 Å distance threshold, and those with at least 5 contacts are shown in the <A HREF="#MmdbsrvThumbnailSchematic">interaction schematic</A> on the <A HREF="#SummaryPage">structure summary page</A>.<!-- Å is the HTML code for Angstrom, <20> --><BR><BR>
|
||
|
||
<A NAME="DataProcessingInteractionsIons"></A>
|
||
<A NAME="DataProcessingInteractionsCrystallizationAgents"></A>
|
||
<I>Note: <B>Ions</B> that interact with the biomolecules in the structure but do not reach the 5 contact threshold will be absent from the interaction schematic; however, they will be listed in the tabular summary of <A HREF="#MmdbsrvMolecularComponents">molecular components</A>. Interactions for short peptides, or for molecule types other than protein, DNA/RNA, and chemical, are not calculated. Molecules, such as crystallization agents, etc., that are not part of the biologically active molecule are absent from both the interaction schematic and the molecular components list.</I><!-- Click on any node in the interaction schematic, or on the "explore interactions" link for that molecule in the tabular list of components, to open a detailed view of the interactions between that molecule and others. In the detailed view, triangles indicate the contact points between the molecule being viewed and the other molecules. --> </TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingInteractions________"><B>___header____</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">__________________________________________________________</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingInteractions"><B>{interactions and oligomeric states}</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">{The MMDB data processing procedure calculates distances between atoms in the structure's <A HREF="#MmdbsrvMolecularComponents">molecular components</A> (proteins, RNA molecules, DNA molecules, bound chemicals) to infer <B>interactions</B> among the components, <B>biological units</B> within the structures (oligomeric forms), and identify <B>binding sites</B>.}</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
<P class="indent20 NormalText"> </P>
|
||
<!-- P class="indent20 NormalText"> </P -->
|
||
|
||
<!-- ============ END_DATA_PROCESSING_INTERACTIONS ============ -->
|
||
|
||
<!-- ============ DATA_PROCESSING_GEOMETRICAL_FEATURES ============ -->
|
||
|
||
<A NAME="DataProcessingGeometricalFeatures"></A>
|
||
<P><B>Identify geometrical features</B>:<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
|
||
<!-- P class="indent20">Introductory text, if needed.</P -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingSecondaryStructures"><B>secondary structures</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">Secondary structures (alpha helices and beta strands, as shown in the <I><A HREF="#FourLevelsOfStructure"><span style="color:#d70000">illustration</span></A></I> on four levels of structure) in each protein molecule are identified algorithmically using purely geometric criteria, and the residue span of each secondary structure is noted in the MMDB record. <I>(Note that because the spans are identified algorithmically, they might differ from the secondary structure residue spans annotated in the original PDB file by the data submitter.)</I></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessing3dDomains"><B>3D domains</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">3D domains are compact structural units within a protein that are identified automatically during MMDB data processing using purely geometric criteria. A protein molecule can contain one or more 3D domains, which often correspond with <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains <I>(<span style="color:#d70000">illustrated example</span>)</I></A> observed in molecular evolution. Additionally, proteins that are dissimilar in sequence might contain geometrically similar 3D domains, indicating a distant homology that cannot be recognized by sequence comparison. 3D domains are used in the identification of <A HREF="#DataProcessingSimilarStructuresVAST">VAST similar structures</A>. They are also displayed as footprints on individual protein molecules (<!-- A HREF="#MmdbsrvProteins" --><A HREF="#MmdbsrvProteinsShowAnnotation"><I><span style="color:#d70000">illustrated example</span></I></A>, <A HREF="#MmdbsrvProteins3dDomains">additional details</A>) in the graphical portion of <A HREF="#SummaryPage">structure summary pages</A>.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingInteractions"><B>{interactions and oligomeric states}</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">{The MMDB data processing procedure calculates distances between atoms in the structure's <A HREF="#MmdbsrvMolecularComponents">molecular components</A> (proteins, RNA molecules, DNA molecules, bound chemicals) to infer <B>interactions</B> among the components, <B>biological units</B> within the structures (oligomeric forms), and <B>binding sites</B>.}</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
<P class="indent20 NormalText"> </P>
|
||
<!-- P class="indent20 NormalText"> </P -->
|
||
|
||
<!-- ============ END_DATA_PROCESSING_GEOMETRICAL_FEATURES ============ -->
|
||
|
||
<!-- ============ DATA_PROCESSING_GENES ============ -->
|
||
|
||
<A NAME="DataProcessingGenes"></A>
|
||
<A NAME="DataProcessingGene"></A>
|
||
<P><B>Identify the gene that corresponds to each protein</B>:<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
|
||
<!-- P class="indent20">Introductory text, if needed.</P -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingGeneSymbol"></A><A NAME="DataProcessingGeneSymbols"></A><A NAME="DataProcessingGeneID"></A><B>gene symbols</B></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">A gene symbol, if/as available, appears beside the name of each protein molecule in the tabular list of <A HREF="#MolecularComponents">molecular components</A>. The protein-gene association is determined in the following way:<BR><BR>
|
||
(1) The <A HREF="#SourceDatabases">source database</A>, PDB, provides a <A HREF="http://www.uniprot.org/">UniProt</A> ID for each protein chain in a structure record.<BR><BR>
|
||
(2) The NCBI <A HREF="/gene">Gene database</A> generates data files on its <A HREF="//ftp.ncbi.nih.gov/gene/DATA/">FTP site</A> that provide mappings between protein identifiers and gene identifiers. Specifically: (a) the "gene_refseq_uniprotkb_collab.gz" file lists the correspondence between UniProt and <A HREF="/refseq/">RefSeq</A> protein accessions; and (b) the <!-- "gene2refseq.gz" --> "gene2accession.gz" file lists the correspondence between RefSeq protein accessions and Gene IDs. The MMDB data processing pipeline creates a join between these two tables in order to map each UniProt ID to its corresponding Gene ID, and to link to the NCBI Gene record.<BR><BR>
|
||
<I>(Note that the protein sequence in the structure record is not necessarily identical to the protein product of the gene. For example, a structure record might only contain a fragment of the protein rather than the whole protein. So there is a mapping between the structure's protein molecule and the gene product, but not necessarily an exact sequence match.)</I></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingInteractions"><B>{interactions and oligomeric states}</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">{The MMDB data processing procedure calculates distances between atoms in the structure's <A HREF="#MmdbsrvMolecularComponents">molecular components</A> (proteins, RNA molecules, DNA molecules, bound chemicals) to infer <B>interactions</B> among the components, <B>biological units</B> within the structures (oligomeric forms), and <B>binding sites</B>.}</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
<!-- P class="indent20 NormalText"> </P -->
|
||
|
||
|
||
<!-- ============ END_DATA_PROCESSING_GENES ============ -->
|
||
|
||
|
||
<!-- ============ DATA_PROCESSING_RELATED_STRUCTURES ============ -->
|
||
|
||
<A NAME="DataProcessingSimilarStructures"></A>
|
||
<A NAME="DataProcessingRelatedStructures"></A>
|
||
<P><B>Identify relationships among 3D structures</B>:<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
<BR>
|
||
|
||
<!-- P class="indent20">Introductory text, if needed.</P -->
|
||
|
||
<!-- P class="indent20 MiniText"> </P -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingSimilarStructuresVAST"></A><A NAME="DataProcessingRelatedStructuresVAST"></A><B>find similar 3D structures using VAST algorithm</B></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">The <A HREF="../../VAST/vast.shtml">VAST</A> algorithm is used to identify structures that are similar in 3D shape, regardless of their degree of sequence similarity, in order to identify distant homologs that cannot be recognized by sequence comparison. The region of similarity can span the entire length of a protein molecule, or a portion of it, as indicated by the footprints on the similar structures graphic display. If a structure contains more than one protein molecule, Similar Structures are shown for each one.<BR><BR>
|
||
|
||
In addition, <A HREF="../../vastplus/vastplus.cgi">VAST+</A>, an expanded version of the program, has been applied to each structure in MMDB in order to find macromolecular structures that have similarly shaped <A HREF="#DataProcessingBiologicalForms">biological units</A>, also referred to as "biounits".<BR><BR>
|
||
|
||
Reciprocal links are created among the similar 3D structures and are accessible from the <A HREF="#SummaryPage">structure summary page</A> by either: (a) clicking on the "<!-- A HREF="#LinksSimilarStructures" --><!-- A HREF="#LinksRelatedStructures" --><!-- A HREF="#MmdbsrvRelatedStructures" --><A HREF="#MmdbsrvSimilarStructures">Similar Structures: VAST+</A>" link near the upper right corner of the page; or (b) viewing the <A HREF="#MmdbsrvProteinsShowAnnotation"><B>Protein annotation graphic</B></A> for any protein molecule of interest, then clicking on the bar graphic for the overall <!-- A HREF="#MmdbsrvProteinsShowAnnotation" --><A HREF="#MmdbsrvProteins">protein molecule</A> or for any <A HREF="#MmdbsrvProteins3dDomains">3D domain</A> it contains in order to view a list of other structures that are similar in shape to the molecule or 3D domain you selected.<BR><BR>
|
||
|
||
<I>(Details about VAST and VAST+ are provided in the articles listed on the <A HREF="../../VAST/docs/vast_publications.html">VAST publications</A> page and in the <A HREF="../../VAST/vasthelp.html">VAST help document</A> and <A HREF="../../vastplus/docs/vastplus_help.html">VAST+ help document</A>.)</I>
|
||
|
||
<!-- To retrieve the similar structures, you can either:
|
||
|
||
<UL>
|
||
|
||
<LI>click on the "<A HREF="#MmdbsrvSimilarStructures"><B>Similar Structures</B>: VAST</A>" link near the upper right corner of the summary page. That will open a dialog box listing the individual <A HREF="#MmdbsrvProteins">protein molecules</A> that compose the structure, and the <A HREF="#MmdbsrvProteins3dDomains">3D domains</A> detected in each one. Select a protein molecule or 3D domain of interest to view a list of other structures that are similar in shape to the molecule or 3D domain you selected.<BR>
|
||
<B>OR</B>:</LI><BR>
|
||
|
||
<LI>view the <A HREF="#MmdbsrvProteinsShowAnnotation"><B>protein annotation graphic</B></A> for any protein molecule of interest; and <B>click on the bar graphic</B> for the overall <A HREF="#MmdbsrvProteins">protein molecule</A> or for any <A HREF="#MmdbsrvProteins3dDomains">3D domain</A> it contains in order to view a list of other structures that are similar in shape to the molecule or 3D domain you selected.</LI>
|
||
|
||
</UL -->
|
||
|
||
</TD>
|
||
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD valign="top" class="MiniText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingSimilarStructuresIBIS"></A><A NAME="DataProcessingRelatedStructuresIBIS"></A><B>cluster similar 3D structures by interaction type using IBIS</B></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">The NCBI <A HREF="../../ibis/ibis.cgi">Inferred Biomolecular Interaction Server (IBIS)</A> was developed to categorize interactions observed across numerous experimentally-determined structures that are similar in 3D shape (i.e., across [<A HREF="../../VAST/vast.shtml">]VAST "[<A HREF="#LinksRelatedStructures">]<A HREF="#DataProcessingSimilarStructuresVAST">Similar Structures</A>"), and to infer/predict interacting partners and binding sites by homology. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation.<BR><BR>
|
||
Each protein in MMDB is analyzed using IBIS and similar 3D structures are clustered by the <A HREF="../../ibis/ibis.cgi">IBIS</A> server based on sequence and structural conservation in their binding sites.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" class="MiniText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessing_____"><B>___ItemName___</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">Text text text <A HREF="#_____">link</A> text text text text text text text text text text text text text text text text text text text text text text text text text.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
<!-- P class="indent20 NormalText"> </P -->
|
||
|
||
<!-- P class="indent20">Concluding text, if needed.</P -->
|
||
|
||
<P class="indent20 NormalText"> </P>
|
||
|
||
<!-- ============ END_DATA_PROCESSING_RELATED_STRUCTURES ============ -->
|
||
|
||
<!-- ================= DATA_PROCESSING_CREATE_LINKS ============ -->
|
||
|
||
<A NAME="DataProcessingCreateLinks"></A>
|
||
<P><B>Create links to associated data throughout the Entrez system:</B><img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
<BR>
|
||
|
||
<P class="indent20">As noted in the page on <A HREF="../../structure_discover.html">discovering associations among previously disparate data</A>, the <A HREF="/sites/gquery/"><B>Entrez</B></A> retrieval system is designed to provide integrated access to previously disparate data and make it possible to collect related information on a topic of interest within and across Entrez databases. MMDB therefore identifies such associations during data processing and presents them as "<A HREF="#DocSumLinks">Related Information</A>" menus on <A HREF="#SearchResults">search results</A> pages. Many of the links are also available on <A HREF="#SummaryPage">individual structure records</A>. There are two broad categories of Links:</P>
|
||
|
||
<P class="indent20 MiniText"> </P>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingDirectLinks"><B>direct links</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">Each structure record has <B>one-to-one relationships</B> with specific records in other <A HREF="/sites/gquery">Entrez</A> databases, such as links to the <!-- A HREF="/protein/" --><B>protein</B> sequence, <!-- A HREF="/nuccore/" --><B>nucleotide</B> sequence, and <!-- A HREF="https://pubchem.ncbi.nlm.nih.gov/" --><B>chemical</B> records that were <A HREF="#DataProcessingDeposition">created from</A> the structure's <A HREF="#MmdbsrvMolecularComponents">molecular components</A>.<!-- These include links to the Entrez <A HREF="/protein/">Protein</A>, <A HREF="/nuccore/">Nucleotide</A>, <A HREF="/sites/entrez?db=pcsubstance">PubChem Substance</A>, and <A HREF="/sites/entrez?db=pccompound">PubChem Compound</A> databases, --><BR><BR>
|
||
|
||
A structure record also has links to the <!-- A HREF="/pubmed/" -->PubMed records for <B>articles cited</B> in the structure record and to the <!-- A HREF="/taxonomy/" -->NCBI Taxonomy record(s) for the <B>source</B> <A HREF="#MmdbsrvTaxonomy"><B>organism(s)</B></A>. Reciprocal links between the structure record and these molecular component and literature records are created, making it possible to start in any one of the databases and traverse to associated records in another database.
|
||
<BLOCKQUOTE>
|
||
<B>Example:</B> The structure <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=91866"><B>3Q5S</B> (MMDB ID 91866)</A>: "Crystal Structure of Bmrr Bound to Acetylcholine" is composed of protein and nucleotide molecules and the chemical acetylcholine. The structure therefore has links to the specific <A HREF="/protein/340707835">protein sequence</A>, <A HREF="/nuccore/340707836">nucleotide sequence</A>, <A HREF="https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=187">small molecule</A> records that contain data extracted from the source PDB record for each of those molecular components. In addition, the structure record contains links to the NCBI Taxonomy database record for the source organism, <A HREF="/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=1423"><I>Bacillus subtilis</I></A>, and the to PubMed record <A HREF="/pubmed/21690368">PMID: 21690368</A> for the published reference.
|
||
</BLOCKQUOTE>
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessingIndirectLinks"><B>indirect links</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">Records that are <!-- A HREF="#DataProcessingDirectLinks" -->directly linked to a structure may in turn have associations with other types of data in the Entrez system. Links are therefore also created from the structure record to those additional data types. The methods by which those links are made are explained in more detail in the section on <A HREF="#SearchResults">search results</A>: <A HREF="#DocSumLinks"><B>find related data</B></A><BR><BR>
|
||
|
||
For example, each protein molecule in a structure record was analyzed to <A HREF="#ConservedDomainAnnotations">identify <B>conserved domains</B></A> and infer its function. The structure record will therefore have links to the corresponding <A HREF="/sites/entrez?db=cdd">Conserved Domain Database</A> record(s).<BR><BR>
|
||
|
||
The structure record will have also have links to <B>additional protein sequences</B><!--, beyond the protein sequence data that was extracted from the PDB source file. These additional proteins --> that are cited as cross-references in the "DBREF" record of the PDB source file, to the <!-- A HREF="/gene/" --><B>genes</B> that code for those proteins, and to any other protein sequences that are identical in length, composition, and source organism as the proteins cited in the "DBREF" record of the PDB source file. <I>(The documentation about <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A> provides more information about the various "records" (data fields) that are present in PDB source files.)</I><BR><BR>
|
||
|
||
As final example of an indirect link, if the protein in a structure record is the target of a bioassay, or is involved in the biological process described in the bioassay experiment, a link between the structure record and the <B>biological activity data</B> (<A HREF="/sites/entrez?db=pcassay"><B>PubChem BioAssay</B></A>) is established, if the submitter of the bioassay data provided the link to the structure record's protein.
|
||
<!-- As another example, a structure record that includes a small molecule <A HREF="#MmdbsrvMolecularComponents">component</A> will have a direct link to the <A HREF="/sites/entrez?db=pccompound">PubChem Compound</A> record for that small molecule. If the PubChem Compound record in turn has a link to information about the molecule's biological activity in the <A HREF="/sites/entrez?db=pcassay">PubChem BioAssay</A> Database, a link between the structure record and the BioAssay record will also be established. --><BR><BR>
|
||
|
||
<!-- These types of connections represent indirect (second generation) links and are explained in more detail in the section on <A HREF="#SearchResults">search results</A>: <A HREF="#DocSumLinks">find related data</A>. -->
|
||
<BLOCKQUOTE>
|
||
<B>Example:</B> The structure <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=91866"><B>3Q5S</B> (MMDB ID 91866)</A>: "Crystal Structure of Bmrr Bound to Acetylcholine" includes the protein, "Multidrug-efflux Transporter 1 Regulator," <!-- (<A HREF="/protein/340707835">3Q5S_A</A>) --> which has been annotated with <A HREF="/protein?LinkName=structure_cdd_superfamily_2&from_uid=91866"><!-- A HREF="../../cdd/cdd_help.shtml#Superfamily" -->two conserved domain superfamilies</A><!-- (<A HREF="/protein?LinkName=structure_cdd_superfamily_2&from_uid=91866"><A HREF="/sites/entrez?cmd=search&db=cdd&term=cl02600%5BUID%5D+OR+cl01368%5BUID%5D&dopt=DocSum">HTH_MeRR-SF superfamily and GyrI-like superfamily</A>) -->. There are also <A HREF="/protein?LinkName=structure_protein&from_uid=91866">other protein sequence records</A> linked to the structure (beyond the <!-- A HREF="/protein/340707835">3Q5S_A</A --> protein record that was created directly from the PDB source file) because they were either: (a) cited in the "DBREF" record of the PDB source file; (b) listed in the same Entrez Gene record (<A HREF="/gene?LinkName=structure_gene&from_uid=91866">bmrR, Gene ID 938676</A>) as the protein accession that was cited in the "DBREF" record of the PDB source file; or (c) are identical in length, composition, and source organism as any of the proteins in (a) or (b). Of course, the <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=91866"><B>3Q5S</B></A> structure also has a link to the gene record itself.
|
||
As a final example of an indirect link from a structure record to data in another Entrez [add links to BioAssay data for the PubChem record]
|
||
</BLOCKQUOTE>
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
|
||
<!-- ============ DATA_PROCESSING_SECTION_TEMPLATE ============ -->
|
||
|
||
<A NAME="DataProcessing________"></A>
|
||
<!-- P><B>__________Template_Header____________</B>:<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P>
|
||
|
||
<P class="indent20">Introductory text, if needed.</P>
|
||
|
||
<P class="indent20 MiniText"> </P>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessing________"><B>________</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">__________________________________________________________</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MicroText" colspan="6"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="20" style="white-space: nowrap;"> </TD>
|
||
<TD valign="top" width="10"><LI> </LI></TD>
|
||
<TD valign="top" width="200"><A NAME="DataProcessing________"><B>________</B></A></TD>
|
||
<TD valign="top" width="5"> </TD>
|
||
<TD valign="top">__________________________________________________________</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
<P class="indent20 NormalText"> </P -->
|
||
|
||
<!-- P class="indent20 NormalText"> </P -->
|
||
|
||
<!-- P class="indent20">Concluding text, if needed.</P -->
|
||
|
||
</BLOCKQUOTE> <!-- the whole data processing section is enclosed in a blockquote -->
|
||
|
||
<!-- ================= END_DATA_PROCESSING ===================== -->
|
||
|
||
<!-- ================= LEVEL_1_RECORD_TYPES ==================== -->
|
||
|
||
<A NAME="DataTypes"></A>
|
||
<A NAME="RecordTypes"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Record Types</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
Various types of records are available in the Structure database. For example, it is possible to retrieve structures generated by specific <A HREF="#DataTypeExperimentalMethods">experimental methods</A>, as shown below, or structures that contain specific <A HREF="#DataTypeMolecularComponents">molecule types</A> (e.g., protein, RNA, DNA), as shown in the subsequent illustration. A wide variety of <A HREF="#SearchFields">search fields</A> can be used to retrieve data subsets, such as structures that contain specific <B>counts</B> of <A HREF="#SearchFieldProteinMoleculeCount">protein molecules</A>, <A HREF="#SearchFieldDNAMoleculeCount">DNA molecules</A>, <A HREF="#SearchFieldRNAMoleculeCount">RNA molecules</A>, or <A HREF="#SearchFieldChemicalCount">bound chemicals</A> in their <A HREF="#DataProcessingBiologicalForms">biological units</A>. (A separate file shows <A HREF="mmdb_how_to_search_by_chemical.html">how to retrieve 3D protein structures bound to a <B>specific</B> chemical</A>.)
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- =========== LEVEL_2_RECORD_TYPES_BY_EXPERIMENTAL_METHOD =========== -->
|
||
|
||
<A NAME="DataTypeExperimentalMethods"></A>
|
||
<A NAME="ExperimentalMethodsIllustration"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" width="100%" class="format1H" colspan="3"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A><B>Experimental methods</B></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="Top"><B>X-ray crystallography</B> determines the arrangement of atoms within a protein by passing X-rays through a crystallized form of the protein and analyzing the resulting X-ray diffraction pattern. This technique provides the highest resolution and usually yields only one model of a structure. <B>Nuclear magnetic resonance (NMR)</B> determines the structure of a protein in solution and generally yields multiple models, which allow for characterization of the biomolecule's motion in solution. <B>Additional experimental methods</B>, such as neutron diffraction, electron microscopy, and more, are listed in the <A HREF="#SearchFieldExpMethod">ExpMethod</A> search field, which can be browsed by using the <A HREF="#SearchMethodShowIndex">Show index</A> link on the Advanced Search page.</TD>
|
||
|
||
<TD class="format1B" valign="Top" width="300">
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=69148"><IMG src="images/xray_3D07_B.png" height="350" width="300" border="0" alt="X-Ray crytallography structure of Human P53 Core Domain With Hot Spot Mutation R249s (MMDB ID 69148, PDB ID 3D07), Protein Molecule B, showing alpha helix (green) and beta strand (yellow) secondary structures, disordered regions (blue), and Zinc ion. Click on this image to open the MMDB record, which provides access to the corresponding publication and interactive views of the structure in Cn3D."></A>
|
||
</TD>
|
||
|
||
<TD class="format1B" valign="Top" width="300">
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=37352"><IMG src="images/nmr_2FEJ.png" height="350" width="300" border="0" alt="NMR (Solution) Structure Of Human P53 Dna Binding Domain (MMDB ID 37352, PDB ID 2FEJ). Click on this image to open the MMDB record, which provides access to the corresponding publication and interactive views of the structure in Cn3D. Select the Drawing: All Models option on the MMDB record before pressing the Structure View in Cn3D button to generate this view."></A>
|
||
</TD>
|
||
|
||
<!-- TD class="format1B" valign="Top" width="300">
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=___"><IMG src="images/________" height="350" width="300" border="0" alt="________. Click on this image to open the MMDB record, which provides access to the corresponding publication and interactive views of the structure in Cn3D."></A>
|
||
</TD -->
|
||
|
||
</TR>
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- ========== LEVEL_2_RECORD_TYPES_BY_MOLECULAR_COMPONENTS ========== -->
|
||
|
||
<A NAME="DataTypeMolecularComponents"></A>
|
||
<A NAME="DataTypeMoleculeTypes"></A>
|
||
<A NAME="MoleculeTypesIllusrtation"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" width="100%" class="format1H" colspan="4"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A><B>Molecule Types</B></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="Top">The biomolecules in MMDB can be <A HREF="#MmdbsrvMolecularComponents">composed</A> of <B>protein</B> molecules, <B>RNA</B> molecules, <B>DNA</B> molecules, as in the examples shown here, or <B>combinations</B> of these components, as shown in the earlier illustration of the <A HREF="#WhatIs">P53 Tumor Suppressor</A>.<BR><BR>
|
||
Structures can also contain <B>bound chemicals</B>, as shown in the earlier illustration of ovine <A HREF="#DatabaseApplications">prostaglandin H2 synthase</A>.
|
||
</TD>
|
||
|
||
<TD class="format1B" valign="Top" width="200">
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=66539"><IMG src="images/prot_2K4T_membrane_protein.png" height="250" width="200" border="0" alt="Protein structure example: Human (membrane protein) Vdac-1 In Ldao Micelles (MMDB ID 66539, PDB ID 2K4T). Click on this image to open the MMDB record, which provides access to the corresponding publication and interactive views of the structure in Cn3D."></A>
|
||
</TD>
|
||
|
||
<TD class="format1B" valign="Top" width="200">
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=52188"><IMG src="images/rna_1Z31_telomerase_rna.png" height="250" width="200" border="0" alt="RNA structure example: Enzyme-Activating Fragment Of Human Telomerase Rna (MMDB ID 52188, PDB ID 1Z31). Click on this image to open the MMDB record, which provides access to the corresponding publication and interactive views of the structure in Cn3D."></A>
|
||
</TD>
|
||
|
||
<TD class="format1B" valign="Top" width="200">
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=53263"><IMG src="images/dna_2GKU_telomere_dna_tetraplex.png" height="250" width="200" border="0" alt="DNA structure example: Monomeric Human Telomere Dna Tetraplex With 3+1 Strand Fold Topology, Two Edgewise Loops And Double-Chain Reversal Loop, Nmr, 12 Structures (MMDB ID 53263, PDB ID 2GKU). Click on this image to open the MMDB record, which provides access to the corresponding publication and interactive views of the structure in Cn3D."></A>
|
||
</TD>
|
||
|
||
<!-- TD class="format1B" valign="Top" width="200">
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=___"><IMG src="images/________" height="250" width="200" border="0" alt="________. Click on this image to open the MMDB record, which provides access to the corresponding publication and interactive views of the structure in Cn3D."></A>
|
||
</TD -->
|
||
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="100%" class="format1A" colspan="4">
|
||
Structures containing <B>specific molecule types</B> (e.g., proteins, DNA, RNA, and/or chemicals) can be retrieved using the <B>blue buttons</B> on the <A HREF="/structure">Entrez Structure</A> search page or the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resource group page, or by using the technique described in <A HREF="mmdb_how_to_search_by_molecule_type.html">How to retrieve 3D structures for a specific type of molecule</A>. Structures that contain <B>bound chemicals</B> can be retrieved by using the <A HREF="#SearchFieldChemicalCount">Chemical Count</A> search field or the method described in <A HREF="mmdb_how_to_search_by_chemical.html">How to find 3D protein structures bound to a specific chemical</A>.
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
|
||
<!-- ================= LEVEL_1_UPDATE_FREQUENCY ==================== -->
|
||
|
||
<A NAME="DataProcessingUpdateFrequency"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Update Frequency</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
The <A HREF="../mmdb.shtml">Molecular Modeling DataBase (MMDB)</A> is updated on a weekly basis with new structures <A HREF="#SourceDatabases">imported</A> from the <SPAN class="ThumbText"><A HREF="http://www.rcsb.org/pdb/"><B>RCSB Protein Data Bank (PDB)</B></A></SPAN>. All newly added structures go through the <A HREF="#DataProcessing">data processing</A> procedures described above.<BR><BR>
|
||
|
||
In addition, <A HREF="#DocSumLinks">links to related data</A> are updated on a regular basis for all structures in the database. This ensures that new data in other <A HREF="/sites/gquery/">Entrez</A> databases are reciprocally linked to 3D structures. <!--For example, as new sequences are deposited into the <A HREF="/protein/">Entrez Protein</A> database, the <A HREF="../mmdb.shtml#CBLAST">CBLAST</A> program is used to create links from those proteins to existing and/or new 3D structures that are similar in sequence (available as A HREF="#LinkFromOtherDatabase" <A HREF="#LinksFromProteinToStructure">Related Structures</A> from the links menu of protein sequence records; <A HREF="mmdb_how_to_search_by_gene.html"><span style="color:#d70000">illustrated example</span></A>).--><BR><BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
|
||
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ====== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ############ -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ############### BLUE_HEADER_SECTION_4_INPUT_SEARCH_TIPS ################### -->
|
||
|
||
<A NAME="SearchTips"></A>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Search Tips</SPAN></TD>
|
||
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############# END_BLUE_HEADER_SECTION_4_INPUT_SEARCH_TIPS ################# -->
|
||
|
||
|
||
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_4_CONTENTS ########### -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
||
<TR>
|
||
<TD class="WhiteCellBlueEdgeAll">
|
||
|
||
<!-- ============ MINI_TOC FOR SEARCH METHODS ============== -->
|
||
|
||
<BR>
|
||
<BLOCKQUOTE>
|
||
| <A HREF="#SearchTipsInputValues">allowable search terms</A> | <A HREF="#SearchMethods">search methods</A> | <A HREF="#SearchFields">search fields</A> | <A HREF="#SearchTipsQuotes">use of quotes</A> | <A HREF="#SearchTipsTruncation">wild card *</A> |<BR>
|
||
| <A HREF="#SearchMethodBasic">basic search</A> | <A HREF="#SearchDetails">search details</A> | <A HREF="#SearchMethodLimits">limits</A> |<BR>
|
||
| <A HREF="#SearchMethodAdvanced">advanced search</A> | <A HREF="#SearchBuilder">search builder</A> | <A HREF="#SearchMethodShowIndex">show index list</A> | <!--A HREF="#SearchMethodPreview">preview</A> | --> <A HREF="#SearchMethodHistory">history</A> | <A HREF="#SearchMethodComplexBoolean">complex Boolean query</A> | <A HREF="#SearchMethodRangeQuery">range query</A> |<BR>
|
||
| <A HREF="#LinkFromOtherDatabase">link from other Entrez databases to 3D structures</A> | <A HREF="#LinksFromProteinToStructure">links from protein sequence records to 3D structures</A> |
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============ END_MINI_TOC FOR SEARCH METHODS ============== -->
|
||
|
||
<!-- =============== LEVEL_1_ALLOWABLE_INPUT_VALUES =============== -->
|
||
|
||
<A NAME="SearchTipsInputValues"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Allowable search terms</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<A NAME="SearchTipsOtherMethods"></A>
|
||
<BLOCKQUOTE>
|
||
This help document focuses on how to search for 3D macromolecular structures using the <A HREF="/sites/gquery/">Entrez</A> search system, which allows you to retrieve records that contain desired <A NAME="SearchByTextTerm">text terms</A>. <A HREF="mmdb_search.html"><B>Additional search methods</B></A> allow you to search the database with a <B>query protein sequence</B><!--(using <A HREF="../mmdb.shtml#CBLAST"><B>CBLAST</B></A>)--> or with the <B>3D coordinates for a newly resolved structure</B> (using <A HREF="../mmdb.shtml#VAST"><B>VAST</B></A> tool); separate help documents exist for those search systems.<BR><BR>
|
||
|
||
In the <A HREF="/structure">Entrez Structure</A> search interface, you can retrieve structure records by searching for:
|
||
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
|
||
<A NAME="SearchByTextTerm"></A>
|
||
<BLOCKQUOTE>
|
||
<B>text terms (key words)</B>:  A wide variety of text terms, such as names of proteins, bound chemicals, authors, and more can be used to search the Entrez Structure database. You can also search for other words that might be present in any of the other text containing <A HREF="#SearchFields">search fields</A> of a record.<BR>
|
||
Because terminology can vary across records, it can be helpful to include <B>synonyms</B> in your query, for example:
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" class="NormalText" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD width="50" class="NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
|
||
<TD class="NormalText" ALIGN="LEFT" VALIGN="TOP"><LI>suppressor OR inhibitor</LI></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="50" class="NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
|
||
<TD class="NormalText" ALIGN="LEFT" VALIGN="TOP"><LI>NF1 OR neurofibromin OR neurofibromatosis</LI></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="50" class="NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
|
||
<TD class="NormalText" ALIGN="LEFT" VALIGN="TOP"><LI>PTGS1 OR "prostaglandin endoperoxide synthase 1" (see note about use of <A HREF="#SearchTipsQuotes">quotes</A>)</LI></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
It is also possible to search for a word stem by using an <!-- A HREF="#SearchTipsTruncation" --><B>asterisk (*) as a wild card</B>. For example, a search for <A HREF="/sites/entrez?cmd=search&db=structure&term=inhibit*%5BAll%5D&dopt=DocSum"><I>inhibit*</I></A> will retrieve records with terms such as inhibit, inhibited, inhibition, inhibitor, etc. The <A HREF="/books/NBK3837/">Entrez Help</A> document provides additional information about <A HREF="/books/NBK3837/#EntrezHelp.Using_Wild_Cards_or_Query_Tru">truncating</A> search terms in this way.<BR><BR>
|
||
|
||
<A NAME="SearchByUID"></A>
|
||
<B>unique identifiers</B>:  Structure records can be retrieved by searching for their unique identifiers, in the form of an <A HREF="#MmdbsrvMMDBID">MMDB ID</A> or <A HREF="#MmdbsrvPDBID">PDB ID</A>, or for the unique identifiers of their <A HREF="#MmdbsrvMolecularComponents">molecular components</A>, such as protein sequence <A HREF="/Sitemap/samplerecord.html#GIpB">GI numbers</A> or <A HREF="/Sitemap/samplerecord.html#AccessionB">accession numbers</A>, PubChem <A HREF="https://pubchem.ncbi.nlm.nih.gov/docs/subcmpd_summary_page_help.html#MoleculeCID">compound identifiers (CIDs)</A> or <A HREF="https://pubchem.ncbi.nlm.nih.gov/docs/subcmpd_summary_page_help.html#MoleculeSID">substance identifiers (SIDs)</A>, or external registry names such as Enzyme Commission or chemical registry numbers (EC/RN numbers).<BR><BR>
|
||
|
||
<A NAME="SearchByOrganism"></A>
|
||
<B>organism</B>:  To retrieve structure records for a specific organism or organism group, you can enter its common name (e.g., human) or scientific name (e.g., <I>Homo sapiens</I>), or other taxonomic node (e.g, Primates) in the <A HREF="#SearchFieldOrganism">Organism</A> [orgn] search field. Note that some structure records contain protein or nucleotide sequences from more than one organism, and they will be retrieved if they contain one or more sequences from the organism or taxon specified in your query. If you specifically want to retrieve structure records that contain data from more than one source organism, simply enter the desired organism names with a Boolean AND (e.g., <A HREF="/sites/entrez?cmd=search&db=structure&term=%22human%22%5BOrganism%5D+AND+HIV1%5BOrganism%5D&dopt=DocSum"><I>human[orgn] AND HIV1[orgn]</I></A>).<BR><BR>
|
||
|
||
<A NAME="SearchByDatabaseSubset"></A>
|
||
<B>database subset</B>:  It is possible to retrieve subsets of records that have certain <A HREF="#DataTypes">attributes</A>, such as structures generated by specific <A HREF="#DataTypeExperimentalMethods">experimental methods</A> or containing specific <A HREF="#DataTypeMolecularComponents">molecule types</A> (protein, DNA, RNA) or <A HREF="mmdb_how_to_search_by_chemical.html">bound chemicals</A>.
|
||
Additionally, the <A HREF="#SearchFieldFilter">Filter</A> field allows you to limit a search to records that have links to another Entrez database of interest. For example, a search for <I>structure_biosystems[filter]</I> will retrieve structure records that have links to the <A HREF="/biosystems/">NCBI BioSystems</A> database; a search for <I>structure_omim[filter]</I> will retrieve structure records that have links to the <A HREF="/sites/entrez?db=omim">Online Mendelian Inheritance in Man (OMIM)</A> database; and a search for <I>structure_biosystems[filter] AND structure_omim[filter]</I> will retrieve the subset of records that have links to both of those databases.<BR><BR>
|
||
|
||
<A NAME="SearchByOther"></A>
|
||
<B>and more...</B>  The <A HREF="/sites/entrez?db=structure">Structure</A> database can also be searched by terms that appear in any of the other <A HREF="#SearchFields">search fields</A>.<BR><BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
|
||
<!-- ================= LEVEL_1_SEARCH_METHODS ==================== -->
|
||
|
||
<A NAME="SearchMethods"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Search Methods</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
A variety of techniques can be used to search the database, offering varying degrees of control over your query. In some cases, they offer alternative ways of executing the same search (as is true for sample searches #4, #5, and #6 below), with each method offering different benefits. The search methods include:
|
||
<UL>
|
||
<LI><A HREF="#SearchMethodBasic">Basic search</A> (& <A HREF="#SearchDetails">search details</A>)</LI>
|
||
<LI><A HREF="#SearchMethodLimits">Limits</A></LI>
|
||
<LI><A HREF="#SearchMethodAdvanced">Advanced search</A> (<A HREF="#SearchBuilder">Search builder</A>, <A HREF="#SearchMethodShowIndex">Show index list</A>, <!--A HREF="#SearchMethodPreview">Preview</A --><A HREF="#SearchMethodHistory">History</A>)</LI>
|
||
<!-- UL>
|
||
<A HREF="#SearchBuilder">search builder</A>
|
||
<LI><A HREF="#SearchMethodPreviewIndex">show index</A></LI>
|
||
<LI>preview</LI>
|
||
<LI><A HREF="#SearchMethodHistory">history</A></LI>
|
||
</UL -->
|
||
<LI><A HREF="#SearchMethodComplexBoolean">Complex Boolean query</A></LI>
|
||
<LI><A HREF="#SearchMethodRangeQuery">Range search</A> (range of values in numerical fields such as dates, counts, and resolution<!-- {as well as range searches of molecular weights in 3D Domains database} -->).</LI>
|
||
</UL>
|
||
</BLOCKQUOTE>
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="black 1px" cellpadding="4" class="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD class="format1H" width="10%" align="left"><b>Method</b></TD>
|
||
<TD class="format1H" align="center"><b>Description</b></TD>
|
||
<TD class="format1H" align="center"><b>Example</b></TD>
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="Basic"></A><A NAME="SearchMethodBasic"></A><A NAME="SearchStyleBasic"></A><B>Basic Search</B></TD>
|
||
|
||
<TD class="format1B" valign="top">
|
||
|
||
<LI>Just enter search terms without specifying search fields, other limits, or Boolean operators.</LI><BR><BR>
|
||
|
||
<LI><A NAME="Details"></A><A NAME="SearchDetails"></A>The "<B>Search Details</B>" box in the right margin of the search results page shows exactly how Entrez parsed and handled your query. If desired, you can edit the query in that box and press the "Search" button to run the modified query.<BR><BR>
|
||
|
||
The "<B>See more...</B>" link a the bottom of the "Search Details" box opens a more detailed display:
|
||
<!-- img SRC="../../IMG/spacer.gif" width="150" height="10" border="0"><BR>
|
||
[<A HREF="/books/NBK3827/#pubmedhelp.Displaying_the_Searc"><A HREF="/books/NBK3837/#EntrezHelp.Search_Details_Shows_Query_In">]<img SRC="../../IMG/entrez/entrez_details.png" width="68" height="25" border="0" align="left" alt="image of the Details folder tab">[</A>]<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="150" height="10" border="0"></IMG --></LI>
|
||
<UL>
|
||
<LI>The <B>Query Translation</B> box shows the search strategy used to run the search</LI>
|
||
<UL>
|
||
<LI>To edit the search in the Query Translation box, add or delete terms and then click Search.</LI>
|
||
<LI>Click URL to display the current search as a URL to bookmark for future use. Searches created using History numbers can not be saved using the URL feature.</LI>
|
||
<LI>You may also save your search using <A HREF="/books/NBK3842/"><!-- A HREF="/books/NBK3827/#pubmedhelp.My_NCBI" -->My NCBI</A>.</LI>
|
||
</UL>
|
||
<LI>The <B>Result</B> number link retrieves the documents found and displays them in a search results page.</LI>
|
||
<LI><B>Translations</B> details how each term was translated using Entrez's search rules and syntax for the database.</LI>
|
||
<LI><B>User Query</B> shows the search terms as you entered them in the search box and any syntax errors with the query.</LI>
|
||
<!-- LI>If your last action was displaying related article citations or selected items in another format, Details will indicate this rather than the last query.</LI -->
|
||
<!-- LI>__________</LI -->
|
||
</UL>
|
||
</LI>
|
||
|
||
</TD>
|
||
|
||
<TD class="format1B" valign="top" width="35%">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<B>Search #1</B>:<!-- of the <A HREF="/sites/entrez?db=structure">Structure</A> database --><BR><BR>
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=human+p53+tumor+suppressor&dopt=DocSum"><B>human p53 tumor suppressor</B></A><BR><BR>
|
||
will retrieve biosystems with those terms anywhere in the record.<BR><BR>
|
||
Some of the structure records might not contain proteins or nucleotide sequences from human because we did not limit that search term to the <A HREF="#SearchFieldOrganism">Organism</A> search field. In such cases, the term "human" might appear in a comment or some other field of the record.<BR><BR>
|
||
|
||
Similarly, the term p53 tumor suppressor can appear anywhere in the record, and the words may or may not be adjacent to each other in a record, depending on how Entrez parsed the query (as shown in the <B>Search Details</B> for a given search). To force terms to be searched as a phrase, use <A HREF="#SearchTipsQuotes">quotes</A>. To refine your search in other ways, use the <A HREF="#SearchMethodLimits">Limits</A> option or the <A HREF="#SearchMethodAdvanced">Advanced Search</A> methods described below.<BR><BR>
|
||
|
||
<!-- (Note: If a multi-word search string (e.g., <I>p53 tumor suppressor</I>) appears in a phrase dictionary that used by the Entrez search system for a given database, it will be searched as a phrase. If it does not appear in the phrase dictionary, the terms will be searched separated and AND'ed together (e.g., <I>p53 AND tumor AND suppressor</I>). In that case, you can use <A HREF="#SearchTipsQuotes">quotes</A> (e.g., <I>"p53 tumor suppressor"</I>) to force the terms to be searched as a phrase, if desired.) -->
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><P class="indent20"><A NAME="Limits"></A><A NAME="SearchMethodLimits"></A><A NAME="SearchStyleLimits"></A><B>Limits</B></P></TD>
|
||
<TD class="format1B" valign="top">
|
||
<LI>The Limits page allows you to restrict your search in various ways.<BR><BR>
|
||
|
||
<LI>At a minimum, the Limits page displays the list of available <A HREF="#SearchFields">search fields</A>. You can do a separate search for each term or phrase in your query, as shown in sample Search #2 and #3 to the right, and select the desired search field for each one. (If desired, you can then combine the searches by using the <A HREF="#SearchBuilder">Search Builder</A> or <A HREF="#SearchMethodHistory">History</A> section of the <!-- A HREF="#SearchMethodAdvanced" -->Advanced Search<!-- /A --> page.)</LI><BR><BR>
|
||
|
||
<LI>For some databases, the Limits page also provides other commonly used options, as check boxes and/or pull-down menus, for restricting your <A HREF="#SearchResults">search results</A> to records with specific characteristics<!-- (e.g., <A HREF="#DataTypes">types of records</A>) -->. These check boxes and pull-down menus generally represent a commonly used subset of the <!-- search term and/or field --> choices that are available from the Advanced Search page and are placed on the Limits page for easy access. <!-- For example, you can select the "BioSystem Type" radio button for <A HREF="#DataTypeConservedBiosystem">conserved biosystems</A> on the Limits page as a shortcut for adding the following term and search field to your query:   <I>AND "conserved biosystem"[<A HREF="#SearchFieldFilter">Filter</A>]</I --></LI><BR><BR>
|
||
|
||
<LI><B>IMPORTANT NOTE</B>: Once you have used a particular Limit, warning sign will appear near the top of your search results page that indicates which Limit(s) are currently in effect, for example:<BR><BR>
|
||
|
||
<img SRC="../../IMG/entrez/entrez3_warning_limits_activated.png" width="300" height="40" border="0" alt="image of the Limits folder that displays a deactivated check box, showing that the limits you most recently selected for a search are no longer in effect"><BR><BR>
|
||
|
||
Note that the <B>Limit will remain in effect for all subsequent searches in the current database unless you change or remove that limit</B>. In the illustrated example above, any search you do will be limited to the Titles of records, until you remove the limit. <!-- If you remove the limit, you can always select new limits for subsequent searches, if desired. --><BR><BR>
|
||
|
||
<!-- img SRC="../../IMG/entrez/entrez_limits_checkbox_activated.png" width="77" height="26" border="0" alt="image of the Limits folder that displays an activated check box, showing that the limits you most recently selected for a search are still in effect"> activated
|
||
<BR><BR>
|
||
<img SRC="../../IMG/entrez/entrez_limits_checkbox_deactivated.png" width="77" height="26" border="0" alt="image of the Limits folder that displays a deactivated check box, showing that the limits you most recently selected for a search are no longer in effect"> deactivated </LI -->
|
||
<BR><BR>
|
||
</TD>
|
||
|
||
<TD class="format1B" valign="top" width="35%">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<B>Search #2</B>:<BR><BR>
|
||
On the <A HREF="/structure">Entrez Structure</A> search page, click on the <B>Limits</B> link, select the <A HREF="#SearchFieldOrganism">Organism</A> search field, and enter the following query:<BR><BR>
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=human[orgn]&dopt=DocSum"><B>human</B></A><BR><BR>
|
||
and press "GO". That will retrieve only structure records that contain at least one <A HREF="#MmdbsrvMolecularComponents">molecular component</A> (e.g., protein, DNA, or RNA) from human.<BR><BR><BR>
|
||
<B>Search #3</B>:<BR><BR>
|
||
Open the Limits page again and clear your previous search. Change the search field selection to <A HREF="#SearchFieldTitle">Title</A>, enter the following query:<BR><BR>
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=p53+tumor+suppressor[titl]&dopt=DocSum"><B>p53 tumor suppressor</B></A><BR><BR>
|
||
and press "GO". That will retrieve only records containing those terms in the title of a structure record.<BR><BR>
|
||
If desired, you can then combine the searches on the <!-- A HREF="#SearchMethodAdvanced" -->Advanced Search<!-- /A --> page, either by using the <A HREF="#SearchBuilder">Search Builder</A>, as shown in sample Search #4, or by using the <A HREF="#SearchMethodHistory">History</A> section of that page, as shown in sample Search #5.<BR><BR>
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="Advanced"></A><A NAME="SearchMethodAdvanced"></A><A NAME="SearchStyleAdvanced"></A><B>Advanced Search</B></TD>
|
||
<TD class="format1B" valign="top" colspan="2"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
The Advanced Search page allows you to exercise greater control over your search, for example, by enabling you to:
|
||
|
||
<UL>
|
||
<LI><A HREF="#SearchBuilder">Build a search</A> one step at a time<!--, then either press the "Search" button to display the records retrieved by your search, or click on "<A HREF="#SearchMethodPreview">Add to history</A>" if you prefer to simply add the query to your search history and remain on the Advanced Search page to continue building your query -->.</LI>
|
||
<LI><A HREF="#SearchMethodShowIndex">Browse the index</A> of any search field and add term(s) of interest from the index to the active query box at the top of the page.</LI>
|
||
<LI>View your search <A HREF="#SearchMethodHistory">History</A> and combine or subtract searches from each other.</LI>
|
||
</UL>
|
||
|
||
As you build a query, either by using the <A HREF="#SearchBuilder">Search Builder</A>'s pull-down menus, or by using the "Add" links in the "<A HREF="#SearchMethodHistory">History</A>" portion of the page to combine previous searches, the <B>grey text box</B> at the top of the page will display your <B>current query</B>.<BR><BR>
|
||
|
||
You can also manually edit the current query by clicking the <B>"Edit" link</B> beneath the grey text box. That will allow you to type terms/search numbers/etc. directly into the box, add parentheses for nesting if desired, change Boolean operators, etc.<BR><BR>
|
||
|
||
In addition, the following types of advanced searches can be entered in the query box of any Entrez search page (i.e., in the query box of the database's Home page, Limits page, or Advanced Search page):
|
||
|
||
<UL>
|
||
<LI><A HREF="#SearchMethodComplexBoolean">Complex Boolean query</A></LI>
|
||
<LI><A HREF="#SearchMethodRangeQuery">Range Search</A></LI>
|
||
</UL>
|
||
|
||
<!-- This can be done by using the folder tabs:<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="150" height="5" border="0"><BR>
|
||
<A HREF="#SearchMethodLimits"><img SRC="../../IMG/entrez/entrez_limits.png" width="62" height="25" border="0" alt="image of the Limits folder tab; click on the image to read more about using Limits"></A>
|
||
<A HREF="#SearchMethodPreviewIndex"><img SRC="../../IMG/entrez/entrez_previewindex.png" width="111" height="25" border="0" alt="image of the Preview/Index folder tab; click on the image to read more about using Preview/Index"></A>
|
||
<A HREF="#SearchMethodHistory"><img SRC="../../IMG/entrez/entrez_history.png" width="68" height="25" border="0" alt="image of the History folder tab; ; click on the image to read more about using History"></A> or by entering a <A HREF="#SearchMethodComplexBoolean"><B>Complex Boolean query</B></A> or <A HREF="#SearchMethodRangeQuery"><B>Range Search</B></A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="150" height="1" border="0" -->
|
||
</TD>
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><P class="indent20"><A NAME="SearchBuilder"></A><A NAME="SearchMethodPreviewIndex"></A><A NAME="SearchStylePreviewIndex"></A><B>Search Builder</B></P></TD>
|
||
<TD class="format1B" valign="top">
|
||
<!-- img SRC="../../IMG/entrez/entrez_previewindex.png" width="111" height="25" border="0" alt="image of the Preview/Index folder tab"><BR><BR -->
|
||
<LI>The "Search Builder" section of the <A HREF="#SearchMethodAdvanced">Advanced Search</A> page allows you to build your query step by step, adding a new search term and selecting a new search field at each step. It also allows you to <A HREF="#SearchMethodShowIndex">browse the index</A> of any <A HREF="#SearchFields">search field</A> to view the available terms.</LI><BR><BR>
|
||
|
||
<LI>To <B>build a query</B>:
|
||
<BLOCKQUOTE>
|
||
(1) Select the <A HREF="#SearchFields"><B>Search Field</B></A> of interest using the pull-down menu.<BR><BR>
|
||
(2) <B>Type</B> a term(s) in the text box beside the search field menu. <B>Or</B>, use the "<B>Show index list</B>" link to see the index of the search field and select the desired term from the index. <I>(<A HREF="#SearchMethodShowIndex">tips on using the "Show Index List"</A>)</I><BR><BR>
|
||
(3) Select the Boolean operator (AND, NOT, OR) that should precede the term when it is added to the active query at the top of the page.<BR><BR>
|
||
Continue the above steps, as desired, to add more term/search field combinations to your query.
|
||
<!-- (4) Press the "Add to Search Box" button to insert the term[search field] combination into the active query box.<BR><BR>
|
||
Note: The <B>Show Index</B> link allows you to first browse the selected search field's index before adding a term(s) to the active query (see tips below). If multiple terms are selected from the index window, they will be OR'ed together and then appended to your query with whatever Boolean operator you have selected.<BR><BR -->
|
||
</BLOCKQUOTE></LI>
|
||
|
||
<LI>As you use the Search Builder, the <B>grey text box at the top of the page</B> will show your <B>current query</B>.
|
||
|
||
<BLOCKQUOTE>
|
||
You can manually edit the current query by clicking the <B>"Edit" link</B> beneath the grey text box. That will allow you to type terms/search numbers/etc. directly into the box, add parentheses for nesting if desired, change Boolean operators, etc.<BR><BR>
|
||
|
||
Press the <B>Search</B> button to display the records retrieved by your search (i.e., it displays the <A HREF="#SearchResults">search results</A> page).<BR><BR>
|
||
|
||
Click on the <A NAME="SearchMethodPreview"></A>"<A NAME="SearchMethodPreview"></A><B>Add to history</B>" link if you prefer to simply add the query to your search history and remain on the Advanced Search page, where you can continue building your query.<BR>
|
||
</BLOCKQUOTE></LI>
|
||
|
||
<LI><A NAME="SearchMethodShowIndex"></A><A NAME="SearchStyleIndexButtonTips"></A>Tips on using the "<B>Show Index List</B>" function on the Advanced Search page:
|
||
<BLOCKQUOTE>
|
||
The "<B>Show Index List</B>" function allows you to browse the index of any <A HREF="#SearchFields"><B>Search Field</B></A>. If you select a search field and press the "Show Index" link <B>without entering a term</B> in the box, you will be taken to the top of the index. If you <B>enter a term first</B>, you will be taken to the part of the index that contains your term (or the closest alphabetical location, if your term is not present in the index).<BR><BR>
|
||
The <B>number of records</B> that contain the term will appear in parentheses. You can also browse the index to <B>explore the variety of terms available</B> (for example, select "All Fields", enter "Huntington", and click on the "Show Index" link to see additional spellings and/or related terms, such as Huntington disease, Huntington's, Huntington's disease).
|
||
</BLOCKQUOTE>
|
||
<P class="indent40"><img SRC="../../IMG/entrez/entrez_index_button_Entrez3.png" width="350" height="135" border="0" alt="illustration showing how the Index button can be used to view the list of terms that are available in the selected search field"></P>
|
||
<BLOCKQUOTE>
|
||
To <B>select a range of terms</B> from the index, use the <B>Shift key</B> while selecting the first and last term. Then use the AND, OR, or NOT buttons to add that group of terms to the active query.<BR><BR>
|
||
To <B>select multiple terms that do not fall within a continuous range</B> from the index, use the <B>Control key</B> while selecting the terms of interest. Then use the AND, OR, or NOT buttons to add that group of terms to the active query.<BR><BR>
|
||
<I>Note: When multiple terms are selected from the index window, they are OR'ed together within parentheses and then appended to your query with whatever Boolean operator you have selected.</I>
|
||
</BLOCKQUOTE></LI>
|
||
|
||
</TD>
|
||
<TD class="format1B" valign="top" width="35%">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<B>Search #4</B>:<BR><BR>
|
||
|
||
On the <A HREF="/structure">Entrez Structure</A> search page, click on <B>Advanced Search</B> and build your search one step at a time:<BR><BR>
|
||
|
||
<B>(a)</B> Using the first pull-down menu in Search Builder, select the <A HREF="#SearchFieldOrganism">Organism</A> search field and enter the following query:<BR><BR>
|
||
<!-- A HREF="/sites/entrez?cmd=search&db=structure&term=human[orgn]&dopt=DocSum" --><B>human</B><BR><BR>
|
||
and select "AND" as the Boolean operator. That term/search field selection will automatically be displayed in the grey text box at the top of the page, which shows your current query.<BR><BR><BR>
|
||
|
||
<B>(b)</B> Using the second pull-down menu in Search Builder, select the <A HREF="#SearchFieldTitle">Title</A> search field and enter the following query:<BR><BR>
|
||
<!-- A HREF="/sites/entrez?cmd=search&db=structure&term=p53+tumor+suppressor[titl]&dopt=DocSum" --><B>p53 tumor suppressor</B><BR><BR>
|
||
and select "AND" as the Boolean operator. That newest term/search field selection will automatically be added to the grey text box at the top of the page.<BR><BR><BR>
|
||
|
||
<B>(c)</B> Your query will now appear as: <BR><BR>
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=human%5BOrganism%5D+AND+p53+tumor+suppressor%5BTitle%5D&dopt=DocSum"><B>human[Organism] AND p53 tumor suppressor[Title]</B></A><BR><BR>
|
||
|
||
Press the <B>Search</B> button if you want to display the records retrieved by your search (i.e., it displays the <A HREF="#SearchResults">search results</A> page).<BR><BR>
|
||
|
||
Or, click on the "<B>Add to history</B>" link if you prefer to just add the query to your search history and remain on the Advanced Search page, where you can continue building your query.<BR><BR><BR>
|
||
|
||
<I>Note that this search will produce the same results as sample searches #5 and #6. It is simply executed in a different way. That is, you remain on a single query page (Advanced search) and can browse the index of any search field as you build your query one step at a time.</I>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><P class="indent20"><A NAME="History"></A><A NAME="SearchHistory"></A><A NAME="SearchMethodHistory"></A><A NAME="SearchStyleHistory"></A><B>History</B></P></TD>
|
||
<TD class="format1B" valign="top">
|
||
<!-- img SRC="../../IMG/entrez/entrez_history.png" width="68" height="25" border="0" alt="image of the History folder tab"><BR><BR -->
|
||
<LI>The "History" section of the <A HREF="#SearchMethodAdvanced">Advanced Search</A> page displays the searches you have done in the current database.</LI><BR><BR>
|
||
<LI>You can <B>combine or subtract searches from each other</B> by entering the search numbers and the AND, OR, or NOT Boolean operators in the query box, for example: <B>#2 AND #3</B>. If the query contains several search numbers and Boolean operators, the <B>Boolean operators are processed from left to right</B> unless <B>parentheses</B> are used for nesting. If parentheses are used, the portions of the query in parentheses will be processed first, then the remaining Boolean operators will be processed from left to right.</LI><BR><BR>
|
||
<!-- LI>The search numbers might not be consecutive if you have done intervening searches in other databases. This is because search numbers are assigned consecutively to all the searches you have done across the <A HREF="/sites/gquery/">Entrez</A> system, while "Search History" only shows the subset of searches you have done in a particular database.</LI><BR><BR -->
|
||
<LI>Additional details about Search History:</LI>
|
||
<UL>
|
||
<LI>The Search History will be lost after <B>8 hours of inactivity</B>. (To save a search indefinitely, click on the search # and select "<B>Save in</B> <A HREF="/books/NBK3842/"><!-- A HREF="/books/NBK3827/#pubmedhelp.My_NCBI" --><B>My NCBI</B></A>.)</LI>
|
||
<LI>Click "Clear History" to delete all searches from History.</LI>
|
||
<LI>Entrez will move a search statement number to the top of the History if a new search is the same as a previous search.</LI>
|
||
<LI>History search numbers may not be continuous because some numbers are assigned to intermediate processes, such as displaying a citation in another format.</LI>
|
||
<LI>The maximum number of searches held in History is 100. Once the maximum number is reached, PubMed will remove the oldest search from the History to add the most current search.</LI>
|
||
<LI>A separate Search History will be kept for each database, although the search statement numbers will be assigned sequentially for all databases.</LI>
|
||
<LI>PubMed uses cookies to keep a history of your searches. For you to use this feature, your Web browser must be set to accept <A HREF="/books/NBK3827/#pubmedhelp.Cookies">cookies</A>.</LI>
|
||
<LI>Database records that you have copied to the Clipboard are represented by the search number #0, which may be used in Boolean search statements. For example, to limit the records you have collected in the Clipboard to those from human, use the following search: #0 AND human[organism]. This does not change or replace the Clipboard contents.</LI>
|
||
</UL>
|
||
<!-- LI>See the <A HREF="/books/NBK3827/">PubMed help</A> document for <A HREF="/books/NBK3827/#pubmedhelp.Combining_searches_H">additional details about Search History</A>.</LI -->
|
||
</TD>
|
||
<TD class="format1B" valign="top" width="35%">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<B>Search #5</B>:<BR><BR>
|
||
Use the search numbers shown in the "History section" of the advanced search page to combine previous searches (for example, searches #2 and #3 shown above).<BR><BR>
|
||
To do that, you can either:<BR><BR>
|
||
Click on the "<B>Edit</B>" link beneath the grey text box and type in a search statement such as:<BR><BR>
|
||
|
||
<!-- [<FONT color="0066CC">]<FONT color="336699"><B>#2 AND #3</B></FONT><BR><BR -->
|
||
<!-- span style="color:#0066CC" --><span style="color:336699"><B>#2 AND #3</B></span><BR><BR>
|
||
|
||
Or, instead of typing the search statement, use the "<B>Add</B>" link beside any search number in the "<B>History</B>" section of the Advanced Search page to add that search number into the grey text box.<BR><BR>
|
||
|
||
That will retrieve only records that contain <I>human</I> in the <A HREF="#SearchFieldOrganism">Organism</A> field (i.e., records that contain at least one <A HREF="#MmdbsrvMolecularComponents">molecular component</A> -- protein, DNA, or RNA -- from human) and <I>p53 tumor suppressor</I> in the <A HREF="#SearchFieldTitle">Title</A> field. Compare the retrieval from this search with that of the sample <A HREF="#SearchMethodBasic">basic</A> search above.<BR><BR>
|
||
<I>(Note that your search numbers might be different from those shown here, if you did earlier searches in the Entrez system before trying these examples.)</I><BR><BR>
|
||
<!-- Note that sample searches #5 and #6 provide alternative ways of doing the same search. -->
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="ComplexBoolean"></A><A NAME="SearchMethodComplexBoolean"></A><A NAME="SearchStyleComplexBoolean"></A><B>Complex Boolean</B></TD>
|
||
<TD class="format1B" valign="top">
|
||
Whether you are on the <A HREF="#SearchMethodBasic">Basic search</A> page (i.e., the database's home page), the <A HREF="#SearchMethodLimits">Limits</A> page, or the <A HREF="#SearchMethodAdvanced">Advanced search</A> page, you can:<BR><BR>
|
||
|
||
<LI>Enter a search in <B>command language</B>, specifying your exact combination of desired search terms, search fields, and Boolean operators, as shown in the examples to the right. The syntax is:<BR><BR>
|
||
    <B>term[field] BOOLEAN term[field] BOOLEAN term[field]</B> <I>etc.</I></LI><BR><BR>
|
||
|
||
<LI><A HREF="#SearchFields"><B>Search Field</B></A> names must be placed in <B>square brackets []</B>, and can be written as either the full name, for example, <!-- A HREF="#SearchFieldDatabase" -->[Database], or as the corresponding <!-- A HREF="#SearchFields" -->search field abbreviation<!-- /A -->, for example, [db]  <I>(<A HREF="#SearchFieldTips">additional examples</A>).</I></LI><BR><BR>
|
||
|
||
<LI>Boolean operators (<B>AND</B>, <B>OR</B>, <B>NOT</B>) must be written in <B>UPPER CASE</B>.</LI><BR><BR>
|
||
<LI>Boolean operators are processed from <B>left to right</B> unless parentheses are used for nesting. If <B>parentheses</B> are used, the portions of the query in parentheses will be processed first, then the remaining Boolean operators will be processed from left to right.</LI><BR><BR>
|
||
<LI>Boolean operators can also be used to <B>combine or subtract searches from each other</B> (i.e., to find the union, difference, or intersection of the data sets retrieved by various searches). To do this, use the <A HREF="#SearchMethodHistory"><B>Search History</B></A> section of the Advanced Search page and simply enter the search numbers and desired Boolean operators in the query box.<BR><BR>
|
||
For example, to identify the records that were retrieved by Search #2 of your search history, <B>and</B> also by Search #3, you could enter the following query:<BR><BR>
|
||
#2 AND #3<BR><BR>
|
||
To identify the records that were retrieved by Search #2 but <B>not</B> by Search #3, you could enter the following query:<BR><BR>
|
||
#2 NOT #3</LI><BR><BR>
|
||
</TD>
|
||
<TD class="format1B" valign="top" width="35%">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<B>Search #6</B>:<BR><BR>
|
||
Simply enter all search terms and search fields as a single statement into the query box:<BR><BR>
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=human%5BOrganism%5D+AND+p53+tumor+suppressor%5BTitle%5D&dopt=DocSum"><B>human[Organism] AND p53 tumor suppressor[Title]</B></A><BR><BR>
|
||
Note that this search will produce the same results as sample searches #4 and #5, but it takes only a single step when entered directly into the search box as a Boolean query.<BR><BR><BR>
|
||
<B>Search #7</B>:<BR><BR>
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=%28prostaglandin+H2+synthase+OR+prostaglandin+endoperoxide+synthase%29+NOT+%28%22Primates%22%5BOrganism%5D+OR+%22Rodentia%22%5BOrganism%5D%29"><B>(prostaglandin H2 synthase OR prostaglandin endoperoxide synthase) NOT (primates[Organism] OR rodents[Organism])</B></A><BR><BR>
|
||
This search will retrieve structure records that contain the terms prostaglandin H2 synthase OR prostaglandin endoperoxide synthase in any field, but that will not contain <A HREF="#MmdbsrvMolecularComponents">molecular components</A> (proteins, DNA, RNA) from <A HREF="#SearchFieldOrganism">organisms</A> in the taxonomic orders Primata or Rodentia.
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="RangeSearch"></A><A NAME="RangeQuery"></A><A NAME="SearchMethodRangeQuery"></A><A NAME="SearchStyleRangeQuery"></A><B>Range Search</B></TD>
|
||
<TD class="format1B" valign="top">
|
||
<LI>Range queries are constructed by specifying a lower and upper numerical value separated by a <B>colon (:)</B> to specify the range, followed by a <A HREF="#SearchFields">search field</A> name or abbreviation in square brackets, as shown in the examples to the right. You can insert a space on each side of the colon but that is not necessary; the search will work either way.<BR><BR>
|
||
|
||
All <B>dates</B> and all '<B>counts</B>' (such as residue counts, molecule counts, etc.) fields can be range queried. Apart from that, there are two additional fields that can be range queried: Resolution [RESO] in the Entrez <A HREF="/sites/entrez?db=structure">Structure</A> database, and MolWeight [MWT] in the <A HREF="/protein/">Entrez Protein</A> database (from which you can link to the Structure database).<!-- A HREF="/sites/entrez?db=domains">3D Domains</A> database (which is <A HREF="../mmdb.shtml#3D_Domains">described</A> on the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page) --><BR><BR>
|
||
|
||
<LI>Range queries on <B>Resolutions [RESO]</B> (in angstroms) must have the following format:<BR><BR>
|
||
|
||
     fromResolution <B>:</B> toResolution [RESO]<BR><BR>
|
||
|
||
<LI>Range queries on <B>MolecularWeights [MWT]</B> (in daltons) must have the following format:<BR><BR>
|
||
|
||
     fromMolecularWeight <B>:</B> toMolecularWeight [MWT]<BR><BR>
|
||
|
||
Note that searches by molecular weight are currently possible only in the <A HREF="/protein/"><B>Entrez Protein</B></A> database. When you are searching that database, simply append "AND srcdb_pdb[prop]" to your query if you want to retrieve only the protein sequences that were derived from 3D structure records. For example:<BR><BR>
|
||
|
||
     <B>_____:_____[molwt] AND srcdb_pdb[prop]</B><BR><BR>
|
||
|
||
That will retrieve protein sequences that fall within the specified molecular weight range and that were <A HREF="#DataProcessingDeposition">derived from</A> Protein Data Bank (PDB), the <A HREF="#SourceDatabases">source database</A> for 3D structure records. A specific example is provided in <B>Search #10</B> to the right. <BR>
|
||
|
||
<!-- A HREF="/sites/entrez?db=domains">3D Domains</A> database. {If the 3D Domains database will eventually be discontinued, will Molecular weight searching be available in the structure database?} --><BR><BR>
|
||
|
||
<LI>Range queries on <B>Dates</B> have a similar format:<BR><BR>
|
||
|
||
     FromDate <B>:</B> ToDate [fieldname]<BR><BR>
|
||
|
||
Note: The FromDate and ToDate values can specify an exact date, a month, or a year, and are written in the format: YYYY/MM/DD, YYYY/MM, or YYYY. The <A HREF="#SearchFields">search fields</A> summary table includes the names and abbreviations for the various "date" fields.<BR><BR>
|
||
|
||
<LI>Range queries on "<B>counts</B>" have the format:<BR><BR>
|
||
|
||
     FromCount <B>:</B> ToCount [fieldname]<BR><BR>
|
||
|
||
Note: The FromCount and ToCount values are integers. The <A HREF="#SearchFields">search fields</A> summary table includes the names and abbreviations for the various "counts" fields.
|
||
</LI><BR><BR>
|
||
<!-- LI>Text text text text text <A HREF="#____">link</A>.</LI -->
|
||
</TD>
|
||
|
||
<TD class="format1B" valign="top" width="35%">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
|
||
<B>Search #8</B>:<BR><BR>
|
||
<A HREF="/sites/entrez?db=structure&cmd=search&term=001.50%5BResolution%5D+%3A+001.75%5BResolution%5D&dopt=DocSum"><B>001.50 : 001.75[Resolution]</B></A><BR><BR>
|
||
This search of the <A HREF="/structure">Entrez Structure</A> database will retrieve records that have a <A HREF="#SearchFieldResolution">resolution</A> between 1.50 to 1.75 Angstroms.<BR><BR><BR>
|
||
|
||
<B>Search #9</B>:<BR><BR>
|
||
<A HREF="/sites/entrez?db=structure&cmd=search&term=3%5BLigCount%5D+%3A+5%5BLigCount%5D&dopt=DocSum"><B>3 : 5[LigCount]</B></A><BR><BR>
|
||
This search of the <A HREF="/structure">Entrez Structure</A> database will retrieve structures that have three to five different types of <A HREF="#SearchFieldLigCount">ligands</A> (bound chemicals) in their <A HREF="#DataProcessingBiologicalForms">biological unit</A>.<BR><BR>
|
||
(A separate document describes how to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D protein structures bound to a specific chemical</A>.)<BR><BR><BR>
|
||
|
||
<B>Search #10</B>:<BR><BR>
|
||
Search the <A HREF="/protein/">Entrez Protein</A> database for:<BR><BR>
|
||
<A HREF="/sites/entrez?db=protein&cmd=search&term=4060%5Bmolwt%5D+%3A+4075%5Bmolwt%5D+srcdb_pdb%5Bprop%5D&dopt=DocSum"><B>4060 : 4075[Molwt] AND srcdb_pdb[prop]</B></A><BR><BR>
|
||
That will retrieve protein sequences that have a molecular weight between 4060 and 4075 Daltons and that were <A HREF="#DataProcessingDeposition">derived from</A> 3D structure records. Each protein sequence record will have a link to the corresonding structure record. Alternatively, you can select the "<B>Find Related Data:Structure</B>" option in the right margin of the search results page to retrieve the complete set of structure records that corresponds to the set of protein records you retrieved. <I>(more details about <A HREF="#LinksFromProteinToStructure">protein → structure</A> links...)</I>
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="_____"><B>_________</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<LI>Text text text text text <A HREF="#____">link</A>.</LI><BR><BR>
|
||
<LI>Text text text text text <A HREF="#____">link</A>.</LI><BR><BR>
|
||
<LI>Text text text text text <A HREF="#____">link</A>.</LI>
|
||
</TD>
|
||
<TD class="format1B" valign="top" width="35%">
|
||
<B>Search #N</B>:<BR><BR>
|
||
<A HREF="____"><B>sample search</B></A><BR><BR>
|
||
Comments about retrieval with <A HREF="#____">anchor</A> to other part of document.</TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
Additional details about search methods and options are provided in the: (1) <a HREF="/books/NBK3827/">PubMed help document</a> (including information about temporarily saving records from your search results to the <A HREF="/books/NBK3827/#pubmedhelp.Saving_citations_tem">Clipboard</A>); (2) <A HREF="/books/NBK3842/">My NCBI help document</A> (including information about <A HREF="/books/NBK53592/">Saving search strategies</A> and indefinitely saving records from your search results into your My NCBI <A HREF="/books/NBK53590/">Collections</A>); and (3) general <a HREF="/books/NBK3837/">Entrez help document</a>.
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
|
||
<!-- ================= LEVEL_1_SEARCH_FIELDS ==================== -->
|
||
|
||
<A NAME="SearchFields"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Search Fields</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
Search fields can be selected from pop-up menus on either the <A HREF="#SearchMethodLimits"><b>Limits</b></A> or <A HREF="#SearchMethodAdvanced"><b>Advanced Search</b></A> page, or can be typed directly in your query by surrounding field names with <A HREF="#SearchFieldAbbreviations"><b>square brackets []</b></A>, for example, [Organism] or [Orgn].<A HREF="#SearchFieldAbbreviations"><b>*</b></A> The <A HREF="#SearchMethodShowIndex"><b>Show index</b></A> link on the Advanced Search page allows you to <B>browse the index</B> of each search field, where you can see the available terms, the number of records containing each term or phrase, as well as the syntax for entering values in search fields such as dates and EC/RN number.<BR><BR>
|
||
|
||
|
||
The currently available fields include:<BR><BR>
|
||
|
||
<!-- =========== MINI_TOC_LISTING_THE_SEARCH_FIELDS ============== -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0" BGCOLOR="#FFFFFF">
|
||
<TR>
|
||
|
||
<TD WIDTH="33%" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="#SearchFieldAll">All Fields</A><BR>
|
||
<A HREF="#SearchFieldAbstract">Abstract</A><BR>
|
||
<A HREF="#SearchFieldAsuBiopolymerCount">ASU Biopolymer Count</A><BR>
|
||
<A HREF="#SearchFieldAsuDNAMoleculeCount">ASU DNA Molecule Count</A><BR>
|
||
<A HREF="#SearchFieldAsuChemicalCount">ASU Chemical Count</A><BR>
|
||
<A HREF="#SearchFieldAsuOtherMoleculeCount">ASU Other Molecule Count</A><BR>
|
||
<A HREF="#SearchFieldAsuProteinMoleculeCount">ASU Protein Molecule Count</A><BR>
|
||
<A HREF="#SearchFieldAsuRNAMoleculeCount">ASU RNA Molecule Count</A><BR>
|
||
<A HREF="#SearchFieldAuthor">Author</A><BR>
|
||
<A HREF="#SearchFieldBiopolymerCount">BioUnit Biopolymer Count</A><BR>
|
||
<A HREF="#SearchFieldDNAMoleculeCount">BioUnit DNA Molecule Count</A><BR>
|
||
<A HREF="#SearchFieldLigCount">BioUnit Chemical Count</A><BR>
|
||
<A HREF="#SearchFieldBioUnitMolecularWeight">BioUnit Molecular Weight</A><BR>
|
||
<A HREF="#SearchFieldOtherMoleculeCount">BioUnit Other Molecule Count</A><BR>
|
||
<A HREF="#SearchFieldProteinMoleculeCount">BioUnit Protein Molecule Count</A><BR>
|
||
<A HREF="#SearchFieldRNAMoleculeCount">BioUnit RNA Molecule Count</A><BR>
|
||
<!-- A HREF="#SearchFieldChemicalDescription">[<A HREF="#SearchFieldLigDescr">]Chemical Description</A><BR -->
|
||
<A HREF="#SearchFieldChemicalName"><!-- A HREF="#SearchFieldLigName" -->Chemical Name</A><BR>
|
||
<A HREF="#SearchFieldChemicalSynonyms">Chemical Synonyms</A><BR>
|
||
</TD>
|
||
|
||
<TD WIDTH="33%" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="#SearchFieldConservedDomainDatabaseDescription">Conserved Domain Database Description</A><BR>
|
||
<A HREF="#SearchFieldConservedDomainDescription">Conserved Domain Description</A><BR>
|
||
<A HREF="#SearchFieldConservedDomainPSSMID">Conserved Domain PSSMID</A><BR>
|
||
<A HREF="#SearchFieldConservedDomainShortName">Conserved Domain Short Name</A><BR>
|
||
<A HREF="#SearchFieldConservedDomainTitle">Conserved Domain Title</A><BR>
|
||
<A HREF="#SearchFieldConservedDomainSuperfamilyDescription">Conserved Domain Superfamily Description</A><BR>
|
||
<A HREF="#SearchFieldConservedDomainSuperfamilyPSSMID">Conserved Domain Superfamily PSSMID</A><BR>
|
||
<A HREF="#SearchFieldConservedDomainSuperfamilyShortName">Conserved Domain Superfamily Short Name</A><BR>
|
||
<A HREF="#SearchFieldConservedDomainSuperfamilyTitle">Conserved Domain Superfamily Title</A><BR>
|
||
<A HREF="#SearchFieldDNAName">DNA Name</A><BR>
|
||
<A HREF="#SearchFieldECRNnumber">EC/RN Number</A><BR>
|
||
<A HREF="#SearchFieldExperimentalMethod"><!-- A HREF="#SearchFieldExpMethod" -->Experimental Method</A><BR>
|
||
<A HREF="#SearchFieldGeneDescription">Gene Description</A><BR>
|
||
<A HREF="#SearchFieldGeneName">Gene Name</A><BR>
|
||
<A HREF="#SearchFieldFilter">Filter</A><BR>
|
||
<A HREF="#SearchFieldJournal">Journal</A><BR>
|
||
<A HREF="#SearchFieldMMDBEntryDate">MMDB Entry Date</A><BR>
|
||
<A HREF="#SearchFieldMMDBID"><!-- A HREF="#SearchFieldUID" -->MMDB ID</A><BR>
|
||
<A HREF="#SearchFieldMMDBModifyDate">MMDB Modify Date</A><BR>
|
||
</TD>
|
||
|
||
<TD WIDTH="33%" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="#SearchFieldNumberOfPDBRecordsPerStructure">Number of PDB Records per Structure</A><BR>
|
||
|
||
<!--A HREF="#SearchFieldModDNAResCount">ModDNAResCount</A> |
|
||
<A HREF="#SearchFieldModProteinResCount">ModProteinResCount</A> |
|
||
<A HREF="#SearchFieldModRNAResCount">ModRNAResCount</A> | -->
|
||
|
||
<A HREF="#SearchFieldOligomericState">Oligomeric State</A><BR>
|
||
<A HREF="#SearchFieldOrganism">Organism</A><BR>
|
||
<A HREF="#SearchFieldOtherMoleculeName">Other Molecule Name</A><BR>
|
||
<A HREF="#SearchFieldPdbAccession"><!-- A HREF="#SearchFieldPdbAcc" -->PDB Accession</A> <BR>
|
||
<A HREF="#SearchFieldPDBChemicalCode"><!-- A HREF="#SearchFieldLigCode" -->PDB Chemical Code</A><BR>
|
||
<!-- A HREF="#SearchFieldPdbChainCode">PDB Chain Code</A> | -->
|
||
<A HREF="#SearchFieldPdbClass">PDB Class</A><BR>
|
||
<A HREF="#SearchFieldPdbComment">PDB Comment</A><BR>
|
||
<A HREF="#SearchFieldPDBDepositDate">PDB Deposit Date</A><BR>
|
||
<A HREF="#SearchFieldPdbDescription"><!-- A HREF="SearchFieldPdbDescr" -->PDB Description</A><BR>
|
||
<A HREF="#SearchFieldPdbFileCount">PDB File Count</A><BR>
|
||
<A HREF="#SearchFieldPdbSource">PDB Source</A><BR>
|
||
<A HREF="#SearchFieldProteinName">Protein Name</A><BR>
|
||
<A HREF="#SearchFieldResolution">Resolution</A><BR>
|
||
<A HREF="#SearchFieldRNAName">RNA Name</A><BR>
|
||
<A HREF="#SearchFieldTitle">Title</A>
|
||
<!-- A HREF="#______">__________</A> |
|
||
<A HREF="#______">__________</A> |
|
||
<A HREF="#______">__________</A> | -->
|
||
</TD>
|
||
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
<!-- =========== END_MINI_TOC_LISTING_THE_SEARCH_FIELDS ============== -->
|
||
|
||
<BR><BR>
|
||
|
||
<!-- ======== TABLE_OF_SEARCH_FIELDS_ABBREVIATIONS_DESCRIPTIONS ========= -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="black 1px" cellpadding="3" class="format1 TableText1">
|
||
|
||
<tr>
|
||
<td class="format1H"><b>Field name</b></td>
|
||
<td class="format1H" style="white-space: nowrap;"><A HREF="#SearchFieldAbbreviations"><b>Abbreviation*</b></A></td>
|
||
<td class="format1H"><b>Description</b></td>
|
||
<td class="format1H"><b>Sample Search</b></td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldAll"></A>All Fields</td>
|
||
<td class="format1B" valign="Top">[ALL]</td>
|
||
<td class="format1B" valign="Top">Searches the complete database record</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&Term=%22p53+tumor+suppressor%22%5BAll%5D"><b>"p53 tumor suppressor"[all]</b></a> <BR><BR> <!-- Use the escape character %22 in the URL to represent quotes around the phrase. -->
|
||
will retrieve the structure records that contain the phrase "p53 tumor suppressor" in any field of the record.<br><br>
|
||
<I>(Compare these search results with those obtained by the sample <A HREF="#SearchFieldAbstract">Citation Abstract Field</A> search, which will retrieve structure records containing that phrase in the abstract of an associated PubMed record, and with those obtained by the sample <A HREF="#SearchFieldTitle">Title field</A> search, which will retrieve records containing that phrase only in the title of an associated PubMed record.)</I><BR><BR>
|
||
The <A HREF="#SearchTipsQuotes">quotes</A> surrounding the search terms ensure they are searched as a phrase.<A HREF="#SearchTipsQuotes">**</A> <!-- If quotes are not used and the terms are not automatically recognized as a phrase by the Entrez system, Entrez will insert a Boolean AND between the terms and they may or may not appear adjacent to each other in the retrieved records. --></td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldAbstract"></A><A NAME="SearchFieldCitationAbstract"></A>Abstract</td>
|
||
<td class="format1B" valign="Top">[Abstract]<BR>[ABS]<BR>[ABST]</td>
|
||
<td class="format1B" valign="Top">The abstract (if available) of any PubMed reference linked to the structure.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&Term=%22p53+tumor+suppressor%22%5BAbstract%5D"><b>"p53 tumor suppressor"[abstract]</b></a> <BR><BR> <!-- Use the escape character %22 in the URL to represent quotes around the phrase. -->
|
||
will retrieve the structure records that contain the phrase "p53 tumor suppressor" in the abstract of a PubMed reference associated with the structure.<br><br>
|
||
<I>(Compare these search results with those obtained by the sample <A HREF="#SearchFieldAll">All fields</A> search, which will retrieve records containing that phrase in any field of the structure record, and with those obtained by the sample <A HREF="#SearchFieldTitle">Title field</A> search, which will retrieve records containing that phrase only in the structure title.)</I><BR><BR>
|
||
The <A HREF="#SearchTipsQuotes">quotes</A> surrounding the search terms ensure they are searched as a phrase.<A HREF="#SearchTipsQuotes">**</A> <!-- If quotes are not used and the terms are not automatically recognized as a phrase by the Entrez system, Entrez will insert a Boolean AND between the terms and they may or may not appear adjacent to each other in the retrieved records. --></td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldAsuBiopolymerCount"></A>ASU Biopolymer Count</td>
|
||
<td class="format1B" valign="Top">[AsuBiopolymerCount]<BR>[ABPC]<BR>[ASUBPC]</td>
|
||
<td class="format1B" valign="Top">The total number of biopolymers (<A HREF="#SearchFieldAsuProteinMoleculeCount">protein</A>, <A HREF="#SearchFieldAsuDNAMoleculeCount">DNA</A>, and/or <A HREF="#SearchFieldAsuRNAMoleculeCount">RNA</A> molecules) in the raw data for the structure (i.e., in the "<A HREF="#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A>," or "<B>ASU</B>").<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldBioUnitBiopolymerCount">BioUnit Biopolymer Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
<I>Note: Some structures may have a biopolymer count of zero, and can be retrieved by a search for:<BR>    0[AsuBiopolymerCount] <BR>
|
||
These can include structure records that contain only chemicals (such as peptide-like antiobiotics<!-- 2L2X -->), peptide nucleic acids (<A HREF="/pubmed/14512516/">PNAs</A>), or protein or nucleotide sequences composed of ≥ 50% modified amino acids or nucleotides.</I><BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.
|
||
</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3+%3A+8%5BABPC%5D&dopt=DocSum"><b>3 : 8 [ABPC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3%5BABPC%5D+%3A+8%5BABPC%5D&dopt=DocSum"><b>3[ABPC] : 8[ABPC]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3+%3A+8%5BAsuBiopolymerCount%5D&dopt=DocSum"><b>3 : 8[AsuBiopolymerCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from three to eight biopolymers (protein, DNA, and/or RNA) in the raw data (<A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>) for a structure.<!-- BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldBioUnitBiopolymerCount">BioUnit Biopolymer Count</A>.")</I --><BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>3[AsuBiopolymerCount] : 8[AsuBiopolymerCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldAsuDNAMoleculeCount"></A>ASU DNA Molecule Count</td>
|
||
<td class="format1B" valign="Top">[AsuDNAMoleculeCount]<BR>[ADMC]<BR>[ASUDMC]</td>
|
||
<td class="format1B" valign="Top">The number of DNA molecules in the raw data for the structure (i.e., in the "<A HREF="#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A>," or "<B>ASU</B>").<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldBioUnitDNAMoleculeCount">BioUnit DNA Molecule Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2+%3A+6%5BADMC%5D&dopt=DocSum"><b>2 : 6 [ADMC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2%5BADMC%5D+%3A+6%5BADMC%5D&dopt=DocSum"><b>2[ADMC] : 6[ADMC]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2+%3A+6%5BAsuDNAMoleculeCount%5D&dopt=DocSum"><b>2 : 6[AsuDNAMoleculeCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from two to six DNA molecules in the raw data (<A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>) for a structure.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>2[AsuDNAMoleculeCount] : 6[AsuDNAMoleculeCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldAsuChemicalCount"></A><A NAME="SearchFieldAsuLigandCount"></A>ASU Chemical Count</td>
|
||
<td class="format1B" valign="Top">[AsuLigCount]<BR>[ALCT]<BR>[ASULC]</td>
|
||
<td class="format1B" valign="Top">The number of <I>different types</I> of chemicals (not the total number of bound chemicals) in the raw data for the structure (i.e., in the "<A HREF="#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A>," or "<B>ASU</B>"). The bound chemicals are sometimes referred to as "ligands," hence the abbreviation [AsuLigCount].<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldBioUnitLigandCount">BioUnit Ligand Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D structures bound to a specific chemical (e.g., aspirin)</A>.<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3+%3A+5%5BALCT%5D&dopt=DocSum"><b>3 : 5 [ALCT]</b></a>     <I>or</I><BR><BR>
|
||
<A HREF="/sites/entrez?db=structure&cmd=search&term=3%5BALCT%5D+%3A+5%5BALCT%5D&dopt=DocSum"><B>3[ALCT] : 5[ALCT]</B></A>     <I>or</I><BR><BR>
|
||
<A HREF="/sites/entrez?db=structure&cmd=search&term=3%5BAsuLigCount%5D+%3A+5%5BAsuLigCount%5D&dopt=DocSum"><B>3 : 5[AsuLigCount]</B></A><BR><BR>
|
||
will retrieve structures that have three to five different types of bound chemicals (ligands) in their "<A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>" (ASU).<BR><BR>
|
||
(A separate document describes how to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D protein structures bound to a specific chemical</A>.)
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldAsuOtherMoleculeCount"></A>ASU Other Molecule Count</td>
|
||
<td class="format1B" valign="Top">[AsuOtherMoleculeCount]<!-- {{actually is [ASUOtherMoleculeCount]}} --><BR>[AOCT]<BR>[ASUOMC]</td>
|
||
<td class="format1B" valign="Top">The number of molecules in the raw data for the structure (i.e., in the "<A HREF="#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A>," or "<B>ASU</B>") that are <I>not classified as a protein, DNA, RNA, or chemical</I>, and therefore fall into the category of "<I>other</I>." <I>(Compare ASU Other Molecule Count, described here, with "<A HREF="#SearchFieldBioUnitOtherMoleculeCount">BioUnit Other Molecule Count</A>.")</I><BR><BR>
|
||
The "other" molecules are generally <I>non-standard biopolymers</I>. Examples include nucleotide or protein sequences that contain a large percentage of non-standard residues, long sugar chains (e.g., <a href="/Structure/pdb/1HPN">1HPN</a>), artificial constructs that contain a polypeptide backbone and nucleotide side chains (e.g., <a href="/Structure/pdb/1PUP">1PUP</a>), etc.<BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
Additional notes:<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BAOCT%5D&dopt=DocSum"><b>4 : 6 [AOCT]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4%5BAOCT%5D+%3A+6%5BAOCT%5D&dopt=DocSum"><b>4[AOCT] : 6[AOCT]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BASUOtherMoleculeCount%5D&dopt=DocSum"><b>4 : 6[AsuOtherMoleculeCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from four to six protein molecules in the raw data (<A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>) for a structure.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>4[AsuOtherMoleculeCount] : 6[AsuOtherMoleculeCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldAsuProteinMoleculeCount"></A>ASU Protein Molecule Count</td>
|
||
<td class="format1B" valign="Top">[AsuProteinMoleculeCount]<BR>[APMC]<BR>[ASUPMC]</td>
|
||
<td class="format1B" valign="Top">The number of protein molecules in the raw data for the structure (i.e., in the "<A HREF="#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A>," or "<B>ASU</B>").<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldBioUnitProteinMoleculeCount">BioUnit Protein Molecule Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BAPMC%5D&dopt=DocSum"><b>4 : 6 [APMC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4%5BAPMC%5D+%3A+6%5BAPMC%5D&dopt=DocSum"><b>4[APMC] : 6[APMC]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BAsuProteinMoleculeCount%5D&dopt=DocSum"><b>4 : 6[AsuProteinMoleculeCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from four to six protein molecules in the raw data (<A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>) for a structure.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>4[AsuProteinMoleculeCount] : 6[AsuProteinMoleculeCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldAsuRNAMoleculeCount"></A>ASU RNA Molecule Count</td>
|
||
<td class="format1B" valign="Top">[AsuRNAMoleculeCount]<BR>[ARMC]<BR>[ASURMC]</td>
|
||
<td class="format1B" valign="Top">The number of RNA molecules in the raw data for the structure (i.e., in the "<A HREF="#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A>," or "<B>ASU</B>").<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldBioUnitRNAMoleculeCount">BioUnit RNA Molecule Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=6+%3A+10%5BARMC%5D&dopt=DocSum"><b>6 : 10 [ARMC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=6%5BARMC%5D+%3A+10%5BARMC%5D&dopt=DocSum"><b>6[ARMC] : 10[ARMC]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=6+%3A+10%5BAsuRNAMoleculeCount%5D&dopt=DocSum"><b>6 : 10[AsuRNAMoleculeCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from six to ten RNA molecules in the raw data (<A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>) for a structure.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>6[AsuRNAMoleculeCount] : 10[AsuRNAMoleculeCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldAuthor"></A>Author</td>
|
||
<td class="format1B" valign="Top">[AU]<BR>[AUTH]</td>
|
||
<td class="format1B" valign="Top"><!-- The author of the publication that reported the PDB structure findings. -->The name of any author associated with any PubMed reference linked to the structure.<!-- {Are the author names derived from a specific PDB data field or from the PubMed record(s) identified during data processing?} --><BR><BR>
|
||
The format to search this field is: <B>last name</B> followed by a space and up to the first two <B>initials</B> followed by a space and a suffix abbreviation, if applicable, all <B>without periods or a comma</B> after the last name (e.g., <I>o'neil kt[auth]</I> OR <I>o'connell jd 3r[auth]</I>).<BR><BR>
|
||
Entrez automatically truncates on an author's name to account for varying initials, e.g., <I>o'neil k [au]</I> will retrieve o'neil ka, o'neil kt, etc, in addition to o'neil k. To turn off this automatic truncation, enclose the author's name in double <B>quotes</B>, e.g., a search for <I>"o'neil k"[auth]</I> will retrieve just o'neil k.<BR><BR>
|
||
Initials and suffixes may be omitted when searching, if desired. In that case, all authors with the specified last name will be retrieved, regardless of their initials.<BR><BR>
|
||
<!-- {Question/[bug?]:<BR>
|
||
The "Index" function of the Entrez Structure [author] field lists: <BR>
|
||
o'connell j (16) <BR>
|
||
Theoretically, those 16 hits should include all authors with names of o'connell j*, if the author search in MMDB works the same as it does in PubMed. However, when you OR together all the specific variations of o'connell j that were listed in the index (as in search #62 below), you get 23 hits rather than 16. Any idea why that might be happening? In general, a word stem in an Entrez Author index pulls up all records that contain that stem, including the more specific subsets.]<BR><BR>
|
||
Search Most Recent Queries Time Result <BR>
|
||
#63 Search o'connell j[Author] 16:31:08 16 <BR>
|
||
#62 Search (o'connell j[Author] OR o'connell j 3r[Author] OR o'connell jd 3r[Author] OR o'connell jf[Author]) 16:29:20 23 } -->
|
||
</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=pavletich+np[auth]&dopt=DocSum"><b>pavletich np[au]</b></a><BR><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=loll+pj[auth]&dopt=DocSum"><b>loll pj[auth]</b></a><BR><BR><BR>
|
||
will retrieve structure records by those authors</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldBioUnitBiopolymerCount"></A><A NAME="SearchFieldBiopolymerCount"></A>BioUnit Biopolymer Count</td>
|
||
<td class="format1B" valign="Top">[BiopolymerCount]<BR>[BPC]<BR>[BUBPC]</td>
|
||
<td class="format1B" valign="Top">The total number of biopolymers (<A HREF="#SearchFieldBioUnitProteinMoleculeCount">protein</A>, <A HREF="#SearchFieldBioUnitDNAMoleculeCount">DNA</A>, and/or <A HREF="#SearchFieldBioUnitRNAMoleculeCount">RNA</A> molecules) in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldAsuBiopolymerCount">ASU Biopolymer Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
<I>Note: Some structures may have a biopolymer count of zero, and can be retrieved by a search for:<BR>    0[BiopolymerCount] <BR>
|
||
These can include structure records that contain only chemicals (such as peptide-like antiobiotics<!-- 2L2X -->), peptide nucleic acids (<A HREF="/pubmed/14512516/">PNAs</A>), or protein or nucleotide sequences composed of ≥ 50% modified amino acids or nucleotides.</I><BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.
|
||
</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3+%3A+8%5BBPC%5D&dopt=DocSum"><b>3 : 8 [BPC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3%5BBPC%5D+%3A+8%5BBPC%5D&dopt=DocSum"><b>3[BPC] : 8[BPC]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3+%3A+8%5BBiopolymerCount%5D&dopt=DocSum"><b>3 : 8[BiopolymerCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from three to eight biopolymers (protein, DNA, and/or RNA) in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<!-- BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldBioUnitBiopolymerCount">BioUnit Biopolymer Count</A>.")</I --><BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>3[BiopolymerCount] : 8[BiopolymerCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldBioUnitDNAMoleculeCount"></A><A NAME="SearchFieldDNAMoleculeCount"></A>BioUnit DNA Molecule Count</td>
|
||
<td class="format1B" valign="Top">[DNAMoleculeCount]<BR>[DMC]<BR>[BUDMC]</td>
|
||
<td class="format1B" valign="Top">The number of DNA molecules in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldAsuDNAMoleculeCount">ASU DNA Molecule Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2+%3A+6%5BDMC%5D&dopt=DocSum"><b>2 : 6 [DMC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2%5BDMC%5D+%3A+6%5BDMC%5D&dopt=DocSum"><b>2[DMC] : 6[DMC]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2+%3A+6%5BDNAMoleculeCount%5D&dopt=DocSum"><b>2 : 6[DNAMoleculeCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from two to six DNA molecules in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>2[DNAMoleculeCount] : 6[DNAMoleculeCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldBioUnitChemicalCount"></A><A NAME="SearchFieldChemicalCount"></A><A NAME="SearchFieldBioUnitLigandCount"></A><A NAME="SearchFieldLigCount"></A>BioUnit Chemical Count</td>
|
||
<td class="format1B" valign="Top">[LigCount]<BR>[LCNT]<BR>[BULC]</td>
|
||
<td class="format1B" valign="Top">The number of <I>different types</I> of bound chemicals (not the total number of bound chemicals) in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure. The bound chemicals are sometimes referred to as "ligands," hence the abbreviation [LigCount].<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldAsuChemicalCount">ASU Chemical Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D structures bound to a specific chemical (e.g., aspirin)</A>.<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3+%3A+5%5BLCNT%5D&dopt=DocSum"><b>3 : 5 [LCNT]</b></a>     <I>or</I><BR><BR>
|
||
<A HREF="/sites/entrez?db=structure&cmd=search&term=3%5BLCNT%5D+%3A+5%5BLCNT%5D&dopt=DocSum"><B>3[LCNT] : 5[LCNT]</B></A>     <I>or</I><BR><BR>
|
||
<A HREF="/sites/entrez?db=structure&cmd=search&term=3%5BLigCount%5D+%3A+5%5BLigCount%5D&dopt=DocSum"><B>3 : 5[LigCount]</B></A><BR><BR>
|
||
will retrieve structures that have three to five different types of bound chemicals (ligands) in their <A HREF="#DataProcessingBiologicalForms">biological unit</A>.<BR><BR>
|
||
(A separate document describes how to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D protein structures bound to a specific chemical</A>.)
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldBioUnitMolecularWeight"></A>BioUnit Molecular Weight</td>
|
||
<td class="format1B" valign="Top">[MolecularWeight]<BR>[MW]<BR>[MWT]<BR>[MOLWT]<BR>[MolWeight]</td>
|
||
<td class="format1B" valign="Top">The molecular weight of the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") in KiloDaltons (kDa).<BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
 <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldBioUnitOtherMoleculeCount"></A><A NAME="SearchFieldOtherMoleculeCount"></A>BioUnit Other Molecule Count</td>
|
||
<td class="format1B" valign="Top">[OtherMoleculeCount]<BR>[OCNT]<BR>[BUOMC]</td>
|
||
<td class="format1B" valign="Top">The number of molecules in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure that are <I>not classified as a protein, DNA, RNA, or chemical</I>, and therefore fall into the category of "<I>other</I>." <I>(Compare BioUnit Other Molecule Count, described here, with "<A HREF="#SearchFieldAsuOtherMoleculeCount">ASU Other Molecule Count</A>.")</I><BR><BR>
|
||
The "other" molecules are generally <I>non-standard biopolymers</I>. Examples include nucleotide or protein sequences that contain a large percentage of non-standard residues, long sugar chains (e.g., <a href="/Structure/pdb/1HPN">1HPN</a>), artificial constructs that contain a polypeptide backbone and nucleotide side chains (e.g., <a href="/Structure/pdb/1PUP">1PUP</a>), etc.<BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
Additional notes:<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BOCNT%5D&dopt=DocSum"><b>4 : 6 [OCNT]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4%5BOCNT%5D+%3A+6%5BOCNT%5D&dopt=DocSum"><b>4[OCNT] : 6[OCNT]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BOtherMoleculeCount%5D&dopt=DocSum"><b>4 : 6[OtherMoleculeCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from four to six protein molecules in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>4[OtherMoleculeCount] : 6[OtherMoleculeCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top" style="white-space: nowrap;"><A NAME="SearchFieldBioUnitProteinMoleculeCount"></A><A NAME="SearchFieldProteinMoleculeCount"></A>BioUnit Protein Molecule Count</td>
|
||
<td class="format1B" valign="Top">[ProteinMoleculeCount]<BR>[PMC]<BR>[BUPMC]</td>
|
||
<td class="format1B" valign="Top">The number of protein molecules in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldAsuProteinMoleculeCount">ASU Protein Molecule Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BPMC%5D&dopt=DocSum"><b>4 : 6 [PMC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4%5BPMC%5D+%3A+6%5BPMC%5D&dopt=DocSum"><b>4[PMC] : 6[PMC]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BProteinMoleculeCount%5D&dopt=DocSum"><b>4 : 6[ProteinMoleculeCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from four to six protein molecules in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>4[ProteinMoleculeCount] : 6[ProteinMoleculeCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldBioUnitRNAMoleculeCount"></A><A NAME="SearchFieldRNAMoleculeCount"></A>BioUnit RNA Molecule Count</td>
|
||
<td class="format1B" valign="Top">[RNAMoleculeCount]<BR>[RMC]<BR>[BURMC]</td>
|
||
<td class="format1B" valign="Top">The number of RNA molecules in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<BR>
|
||
<I>(Compare with "<A HREF="#SearchFieldAsuRNAMoleculeCount">ASU RNA Molecule Count</A>.")</I><BR><BR>
|
||
This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_molecule_type.html">retrieve all available 3D structures for a specific type of molecule</A> (protein, RNA, DNA, protein+chemical, etc.).<BR><BR>
|
||
In addition, the "Retrieve 3D Structures that have..." blue buttons near the bottom of the <A HREF="../mmdb.shtml">3D Macromolecular Structures</A> resources page and <A HREF="/structure">Entrez Structure</A> search page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=6+%3A+10%5BRMC%5D&dopt=DocSum"><b>6 : 10 [RMC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=6%5BRMC%5D+%3A+10%5BRMC%5D&dopt=DocSum"><b>6[RMC] : 10[RMC]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=6+%3A+10%5BRNAMoleculeCount%5D&dopt=DocSum"><b>6 : 10[RNAMoleculeCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from six to ten RNA molecules in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>6[RNAMoleculeCount] : 10[RNAMoleculeCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<!-- ChemicalDescription will be merged with ChemicalName field because both come from the HETNAM record of PDB source file -->
|
||
<!-- tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldChemicalDescription"></A><A NAME="SearchFieldLigDescr"></A>Chemical Description</td>
|
||
<td class="format1B" valign="Top">[LDES]<BR>[LIGD]<BR>[LDSC]<BR>[LDESC]</td>
|
||
<td class="format1B" valign="Top">The author's brief description of a ligand (bound chemical) in the PDB structure, extracted from the PDB source file. [Because this is a free text field, the terminology used by authors can vary among different structure records.]<BR><BR>
|
||
A separate file provides tips on how to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D structures bound to a specific chemical (e.g., aspirin)</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  [FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________.]
|
||
</td>
|
||
</tr -->
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldChemicalName"></A><A NAME="SearchFieldLigName"></A>Chemical Name</td>
|
||
<td class="format1B" valign="Top">[LNAM]<BR>[LIGN]<BR>[LNAME]</td>
|
||
|
||
<td class="format1B" valign="Top">The name of a ligand (chemical) that is present in a 3D structure record. This was derived from the "HETNAM"* record of the PDB source file and represents the name that the <B>author</B> of the structure used for the chemical.<BR><BR>
|
||
|
||
The same chemical might also be known by <B>other names</B>, which are indexed in the <A HREF="#SearchFieldChemicalSynonyms"><B>Chemical Synonyms</B></A> search field. Use that field if you would like more comprehensive search results.<BR><BR>
|
||
|
||
<!-- {Question: Does PDB use a controlled vocabulary or dictionary of ligand names? Any caveats in using this field?}<BR><BR -->
|
||
For <B>example</B>, the author of the <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1PTH">1PTH</A> structure, used the term "2-HYDROXYBENZOIC ACID"<!-- (and indicated "SALICYLIC ACID" as a synonym), which is not indexed in the chemical name field --> as the chemical name for the aspirin molecule bound to Prostaglandin H2 Synthase. A search of the "Chemical Name" field for "2-Hydroxybenzoic Acid" will therefore retrieve 1PTH (along with other structures in which the authors used the same chemical name). However, if you search the "Chemical Name" field for a term <I>other</I> than the one the author used in the HETNAM record of their PDB source file, you will not retrieve those structures.<BR><BR>
|
||
|
||
<B>For broader search results</B>, use the</B> "<A HREF="#SearchFieldChemicalSynonyms"><B>Chemical Synonyms</B></A>" field instead. That will allow you to enter any one of many names by which a chemical has been known. For example, you could search for either "2-Hydroxybenzoic Acid" or "salicylate" or "2-Carboxyphenol" (or another synonym) and you will retrieve all macromolecular structures that contain <A HREF="https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=338">salicylic acid</A>, regardless of the chemical name that the authors used for it.<BR><BR>
|
||
|
||
A separate file provides additional tips on how to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D structures bound to a specific chemical (e.g., aspirin)</A>.<BR><BR>
|
||
|
||
<!-- The PDB definition of a ligand (bound chemical) in the PDB structure, extracted from the HETNAM record of the PDB source file. -->
|
||
<I>* Note: "HETNAM" is the PDB terminology for "heterogen name," which refers to any non-biopolymer that is present in a 3D structure record. The documentation about <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A> provides more information about the various "records" (data fields), such as HETNAM, that are present in PDB source files.</I><BR><BR>
|
||
|
||
</td>
|
||
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2+hydroxybenzoic+acid[LNAM]&dopt=DocSum"><b>2 hydroxybenzoic acid[LNAM]</b></a><BR><BR>
|
||
will retrieve structure records in which the author used the term "2 hydroxybenzoic acid" as the name of the chemical present in the 3D structure.<BR><BR>
|
||
<I>Tip: To search for other names by which the chemical has been known, such as "salicylate" or "2-Carboxyphenol," use the <A HREF="#SearchFieldChemicalSynonyms">Chemical Synonyms</A> search field.<!-- That field will also include the chemical name used by the author, if that name has been found to consistently refer to the chemical in question. --></I>
|
||
</td>
|
||
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldChemicalSynonyms"></A>Chemical Synonyms</td>
|
||
<td class="format1B" valign="Top">[ChemSyn]<BR>[CSYN]</td>
|
||
<td class="format1B" valign="Top">The various names by which a given chemical structure has been known.<!-- (This field will yield broader search results than the "Chemical Name field.") --><BR><BR>
|
||
|
||
For example, the terms "salicylate," "2-Hydroxybenzoic acid," "o-hydroxybenzoic acid," "2-Carboxyphenol," "o-Carboxyphenol," "2-hydroxy(1-14c)benzoic acid," etc. have been used to refer to the chemical structure of salicylic acid. You can search the "Chemical Synonym" field for <B>any</B> of those terms in order to retrieve <B>all</B> of the 3D macromolecular structures that contain the chemical that is described in the corresponding PubChem Compound record (<A HREF="https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=338">CID 338</A>).<BR><BR>
|
||
|
||
The chemical names in this search field represent the <A HREF="https://pubchem.ncbi.nlm.nih.gov/docs/subcmpd_summary_page_help.html#SynonymsFiltered">filtered synonyms</A> from <A HREF="/pccompound/">PubChem Compound</A> records that correspond to the chemicals present in the 3D macromolecular structure records.<BR><BR>
|
||
|
||
A separate file provides additional tips on how to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D structures bound to a specific chemical (e.g., aspirin)</A>.<BR><BR>
|
||
|
||
<!--The PubChem help document provides additional information on the <A HREF="https://pubchem.ncbi.nlm.nih.gov/docs/subcmpd_summary_page_help.html#DataProcessingSynonyms">various synonyms</A> that have been used for a chemical. -->
|
||
</td>
|
||
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=salicylate[ChemSyn]&dopt=DocSum"><b>salicylate[ChemSyn]</b></a><BR><BR>
|
||
will retrieve 3D macromolecular structure records that contain the chemical shown in the PubChem Compound record for salicylic acid (<A HREF="https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=338">CID 338</A>), regardless of the chemical name that was used by the submitter of the 3D macromolecular structure.<BR><BR>
|
||
This search, for example, will retrieve <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1PTH">1PTH</A> structure (among others), even though the submitter of 1PTH used the term "2-Hydroxybenzoic Acid" instead of the term "salicylate" to refer to the chemical that is bound to Prostaglandin H2 Synthase.
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldConservedDomainDatabaseDescription"></A>Conserved Domain Database Description</td>
|
||
<td class="format1B" align="center" valign="Top" colspan="3"><I>See <A HREF="#SearchFieldConservedDomainSuperfamilyDescription">Conserved Domain Superfamily Description</A></I></td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldConservedDomainDescription"></A>Conserved Domain Description</td>
|
||
<td class="format1B" valign="Top">[CDDF]<BR>[CDSUBDefline]</td>
|
||
<td class="format1B" valign="Top">Any term from the description of a <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domain</A> model.<BR><BR>
|
||
Example:  "<B>sedolisin</B>" is a term in the description of the <A HREF="../../cdd/cdd_help.shtml#CDSource_NCBI_curated">NCBI-curated</A> conserved domain model <A HREF="/Structure/cdd/cddsrv.cgi?uid=cd04056">cd04056</A>, which has the short name "Peptidases_S53," full title "Peptidase domain in the S53 family," and <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> 173788.<BR><BR>
|
||
Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hit</A> to a conserved domain model whose description includes your query term.<BR><BR>
|
||
A separate help document provides additional information about <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=173788[CDID]&dopt=DocSum"><b>sedolisin[CDDF]</b></a><BR><BR>
|
||
will retrieve 3D structures that contain at least one protein molecule annotated with a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hit</A> to a conserved domain whose description includes the term "sedolisin."<BR><BR>
|
||
(For example, it will retrieve 3D structures such as <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1GT9">1GT9</A>: "Thermostable Serine-carboxyl Type Proteinase, Kumamolisin," which contains a protein molecule annotated with <A HREF="/Structure/cdd/cddsrv.cgi?uid=cd04056">cd04056</A>.)
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldConservedDomainPSSMID"></A>Conserved Domain PSSMID</td>
|
||
<td class="format1B" valign="Top">[CDID]<BR>[CDSBID]<BR>[CDSUBID]</td>
|
||
<td class="format1B" valign="Top">The <A HREF="../../cdd/cdd_help.shtml#CD_PSSM">position-specific scoring matrix (PSSM)</A> identifier of a conserved domain that has been annotated as a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hit</A> on one or more protein molecules in a structure.<BR><BR>
|
||
Example:  "<B>173788</B>" is the <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> of the <A HREF="../../cdd/cdd_help.shtml#CDSource_NCBI_curated">NCBI-curated</A> conserved domain model <A HREF="/Structure/cdd/cddsrv.cgi?uid=cd04056">cd04056</A>, which has the short name "Peptidases_S53" and full title "Peptidase domain in the S53 family." <BR><BR>
|
||
Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hit</A> to aconserved domain model bearing the PSSMID of interest.<BR><BR>
|
||
A separate help document provides additional information about <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=173788[CDID]&dopt=DocSum"><b>173788[CDID]</b></a><BR><BR>
|
||
will retrieve 3D structures that contain at least one protein molecule annotated with a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hit</A> to the conserved domain whose <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> is <!-- A HREF="/Structure/cdd/cddsrv.cgi?uid=173788" -->173788.
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldConservedDomainShortName"></A>Conserved Domain Short Name</td>
|
||
<td class="format1B" valign="Top">[CDSN]<BR>[CDSUBName]</td>
|
||
<td class="format1B" valign="Top">The short name of a <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domain</A>. <!-- The short name usually appears in the blue header bar at the top of a <A HREF="../../cdd/cdd_help.shtml#CDVisual">Conserved Domain summary page</A>, to the right of the conserved domain accession number. --><BR><BR>
|
||
Example:  "<B>Peptidases_S53</B>" is the short name of the <A HREF="../../cdd/cdd_help.shtml#CDSource_NCBI_curated">NCBI-curated</A> conserved domain model <A HREF="/Structure/cdd/cddsrv.cgi?uid=cd04056">cd04056</A>, which has the <!--short name "Peptidases_S53," -->full title "Peptidase domain in the S53 family" and <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> 173788.<BR><BR>
|
||
Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hit</A> to a conserved domain model bearing the short name of interest.<BR><BR>
|
||
For a more comprehensive search (for example, to retrieve structures annotated with any domain model that belongs to the Peptidases_S8_S53 <A HREF="../../cdd/cdd_help.shtml#Superfamily">Superfamily</A><!-- cluster (cl* <A HREF="../../cdd/cdd_help.shtml#CDSource_accession_prefix">accessions</A>) -->), please search the <A HREF="#SearchFieldConservedDomainSuperfamilyTitle">Conserved Domain Superfamily Title</A> or <A HREF="#SearchFieldConservedDomainSuperfamilyDescription">Conserved Domain Superfamily Description</A> field instead (using a term such as <I>peptidase</I>) for boader search results.<BR><BR>
|
||
A separate help document provides additional information about <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=Peptidases_S53[CDSN]&dopt=DocSum"><b>Peptidases_S53[CDSN]</b></a> <BR><BR>
|
||
will retrieve 3D structures that contain at least one protein molecule annotated with a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hit</A> to a conserved domain model that the short name of "Peptidases_S53."<BR><BR>
|
||
<I>Note: Query term(s) are not case sensitive, so you can enter your search in upper case, lower case, or mixed case.</I>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldConservedDomainTitle"></A>Conserved Domain Title</td>
|
||
<td class="format1B" valign="Top">[CDDT]<BR>[CDSUBTitle]</td>
|
||
<td class="format1B" valign="Top">
|
||
The title of a conserved domain.<!-- The title usually appears in bold face font right above a conserved domain's description. Not all conserved domains have a title. Some just have a short name and a description. Sometimes the first sentence of a description looks like a title, but it is not actually a "title" unless it appears in bold face font. This is because the title field was added to CDD records in recent years, so older records do not have that field populated.--><BR><BR>
|
||
Example:  "<B>Peptidase domain in the S53 family</B>" is the title of the <A HREF="../../cdd/cdd_help.shtml#CDSource_NCBI_curated">NCBI-curated</A> conserved domain model <A HREF="/Structure/cdd/cddsrv.cgi?uid=cd04056">cd04056</A>, which has the short name "Peptidases_S53"<!-- full title "<B>Peptidase domain in the S53 family</B>," -->and <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> 173788.<BR><BR>
|
||
Note: A search of this field will retrieve 3D structures that contain at least one protein that has been annotated with a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hit</A> to a conserved domain model bearing the title of interest.<BR><BR>
|
||
A separate help document provides additional information about <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=peptidase[CDDT]&dopt=DocSum"><b>peptidase[CDDT]</b></a> <BR><BR>
|
||
will retrieve 3D structures that contain at least one protein molecule annotated with a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hit</A> to a conserved domain model that has the term "peptidase" in its title.<BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldConservedDomainSuperfamilyDescription"></A>Conserved Domain Superfamily Description<BR><BR>
|
||
<I>[Note: this field currently appears as</I> "Conserved Domain Database Description" <I>in the search field menu of the Entrez Structure database]</I></td>
|
||
<td class="format1B" valign="Top">[SPDF]<BR>[CDDSPDefline]<!-- BR>[____]<BR>[____] --></td>
|
||
<td class="format1B" valign="Top">Any term from the description of a <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domain</A> <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamily</A>.<BR><BR>
|
||
Example:  "<B>subtilisin</B>" is a term in the description of the conserved domain superfamily <A HREF="/Structure/cdd/cddsrv.cgi?uid=cl10459">cl10459</A>, which has the short name "Peptidases_S8_S53 Superfamily," full title "Peptidase domain in the S8 and S53 families," and <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> 209143.<BR><BR>
|
||
Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a conserved domain superfamily whose description includes your query term.<BR><BR>
|
||
A separate help document provides additional information about <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=173788[CDID]&dopt=DocSum"><b>subtilisin[SPDF]</b></a><BR><BR>
|
||
will retrieve 3D structures that contain at least one protein molecule annotated with a conserved domain superfamily whose description includes the term "subtilisin."<BR><BR>(For example, it will retrieve 3D structures such as <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1GT9">1GT9</A>: "Thermostable Serine-carboxyl Type Proteinase, Kumamolisin," which contains a protein molecule annotated with <A HREF="/Structure/cdd/cddsrv.cgi?uid=cl10459">cl10459</A>.)
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldConservedDomainSuperfamilyPSSMID"></A>Conserved Domain Superfamily PSSMID</td>
|
||
<td class="format1B" valign="Top">[SFID]<BR>[CDSUPID]</td>
|
||
<td class="format1B" valign="Top">
|
||
The <A HREF="../../cdd/cdd_help.shtml#CD_PSSM">position-specific scoring matrix (PSSM)</A> identifier of a conserved domain <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamily</A> that has been annotated on one or more protein molecules in a structure.<BR><BR>
|
||
Example:  "<B>209143</B>" is the <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> of the conserved domain superfamily <A HREF="/Structure/cdd/cddsrv.cgi?uid=cl10459">cl10459</A>, which has the short name "Peptidases_S8_S53 Superfamily" and full title "Peptidase domain in the S8 and S53 families."<!-- and <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> 209143." --><BR><BR>
|
||
Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a conserved domain superfamily bearing the PSSMID of interest.<BR><BR>
|
||
A separate help document provides additional information about <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=209143[SFID]&dopt=DocSum"><b>209143[SFID]</b></a><BR><BR>
|
||
will retrieve 3D structures that contain at least one protein molecule annotated with a conserved domain superfamily whose <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> is <!-- A HREF="/Structure/cdd/cddsrv.cgi?uid=209143" -->209143.
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldConservedDomainSuperfamilyShortName"></A>Conserved Domain Superfamily Short Name</td>
|
||
<td class="format1B" valign="Top">[SPFN]<BR>[CDDSPName]</td>
|
||
<td class="format1B" valign="Top">The short name of a conserved domain <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamily</A>. <!-- The short name usually appears in the blue header bar at the top of a <A HREF="../../cdd/cdd_help.shtml#CDVisual">Conserved Domain summary page</A>, to the right of the conserved domain superfamily accession number. --><BR><BR>
|
||
Example:  "<B>Peptidases_S8_S53 Superfamily</B>" is the short name of the conserved domain superfamily <A HREF="/Structure/cdd/cddsrv.cgi?uid=cl10459">cl10459</A>, which has the<!-- short name "Peptidases_S8_S53 Superfamily," --> full title "Peptidase domain in the S8 and S53 families" and the <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> 209143." <BR><BR>
|
||
Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a conserved domain superfamily bearing the short name of interest.<BR><BR>
|
||
A separate help document provides additional information about <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=Peptidases_S8_S53[SPFN]&dopt=DocSum"><b>Peptidases_S8_S53[SPFN]</b></a> <BR><BR>
|
||
will retrieve 3D structures that contain at least one protein molecule annotated with a conserved domain superfamily that the short name of "Peptidases_S8_S53."<BR><BR>
|
||
<I>Note: Query term(s) are not case sensitive, so you can enter your search in upper case, lower case, or mixed case.</I>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldConservedDomainSuperfamilyTitle"></A>Conserved Domain Superfamily Title</td>
|
||
<td class="format1B" valign="Top">[SPTL]<BR>[CDDSUPT]</td>
|
||
<td class="format1B" valign="Top">The title of a conserved domain superfamily.<!-- The title usually appears in bold face font right above a conserved domain superfamily's description. Not all conserved domains have a title. Some just have a short name and a description. Sometimes the first sentence of a description looks like a title, but it is not actually a "title" unless it appears in bold face font. This is because the title field was added to CDD records in recent years, so older records do not have that field populated.--><BR><BR>
|
||
Example:  "<B>Peptidase domain in the S8 and S53 families</B>" is the title of the conserved domain <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamily</A> <A HREF="/Structure/cdd/cddsrv.cgi?uid=cl10459">cl10459</A>, which has the short name "Peptidases_S8_S53 Superfamily"<!-- full title "Peptidase domain in the S8 and S53 families," --> and the <A HREF="../../cdd/cdd_help.shtml#CD_PSSM_ID">PSSMID</A> 209143." <BR><BR>
|
||
Note: A search of this field will retrieve 3D structures that contain at least one protein molecule annotated with a conserved domain superfamily bearing the title of interest.<BR><BR>
|
||
A separate help document provides additional information about <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=peptidase[SPTL]&dopt=DocSum"><b>peptidase[SPTL]</b></a> <BR><BR>
|
||
will retrieve 3D structures that contain at least one protein molecule annotated with a conserved domain superfamily that has the term "peptidase" in its title.
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldDNAName"></A>DNA Name</td>
|
||
<td class="format1B" valign="Top">[DNAM]<BR>[DNAME]<BR>[DNAName]</td>
|
||
<td class="format1B" valign="Top">The name of an DNA molecule in a structure record. The names of nucleotide molecules, including DNA and RNA, are derived from the COMPND record of the PDB source file.<BR><BR>
|
||
<I>(The documentation about <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A> provides more information about the various "records" (data fields) that are present in PDB source files.)</I><BR><BR>
|
||
The DNA name often reflects the sequence of nucleotides in the molecule itself.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldECRNnumber"></A>EC/RN Number</td>
|
||
<td class="format1B" valign="Top">[EC]</td>
|
||
<td class="format1B" valign="Top">The <A HREF="http://www.chem.qmul.ac.uk/iubmb/enzyme/">Enzyme Commission (EC)</A> number of the PDB structure, representing the classification of an enzyme based on the chemical reactions it catalyzes. The EC number is extracted from the "COMPND" record (data field) of a PDB file. <!-- {the EC number is provided by the depositor, and a search for EC number only retrieves the subset of records that have been specifically annotated with that number.} --><BR><BR>
|
||
<!-- {Where does the EC number come from -- a specific field in the PDB record? author submitted the info, or PDB assigned it? If user searches with EC number, will s/he retrieve ALL proteins in MMDB that fall under that classification, or only the subset of records that have been specifically annotated with the EC number?}<BR><BR -->
|
||
This field can be queried with the <A HREF="#SearchTipsTruncation">wild-card (*)</A> feature, for example:<BR><BR>
|
||
3.2.1.114 [EC]<BR>
|
||
3.2.1.* [EC]<BR>
|
||
3.2.*.* [EC]<BR>
|
||
3.2.* [EC]<BR><BR>
|
||
and so on. Note the queries <b>3.2.*.* [EC]</b> and <b>3.2.* [EC]</b> will return identical set of PDB structures, so the two queries are equivalent.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3.2.1.114[EC]&dopt=DocSum"><b>3.2.1.114[EC]</b></a> <!--     <I>or</I --><BR><BR>
|
||
<!-- a HREF="/sites/entrez?cmd=search&db=structure&term=%223+2+1+114%22[EC]&dopt=DocSum"><b>3 2 1 114[EC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=%223.2.1.114%22[EC]&dopt=DocSum"><b>"3.2.1.114"[EC]</b></a>     <BR><BR -->
|
||
will retrieve structures classified with that specific enzyme commission number.<BR><BR><BR>
|
||
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3.2.1.*[EC]&dopt=DocSum"><b>3.2.1.*[EC]</b></a><!--     <I>or</I --><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3.2.*.*[EC]&dopt=DocSum"><b>3.2.*.*[EC]</b></a><!--     <I>or</I --><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=3.2.*[EC]&dopt=DocSum"><b>3.2.*[EC]</b></a>    <BR><BR>
|
||
use the <A HREF="#SearchTipsTruncation">wild card (*)</A> to retrieve structure records that contain the digits specified, followed by any other digits. <!-- Note the queries <b>3.2.*.* [EC]</b> and <b>3.2.* [EC]</b> will return identical set of PDB structures, so the two queries are equivalent. --><BR><BR>
|
||
You can click on the <A HREF="#SearchDetails">Details</A> folder tab of a <A HREF="#SearchResults">search results</A> page to see exactly how a query was handled by the Entrez system.<BR><BR>
|
||
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldExperimentalMethod"></A><A NAME="SearchFieldExpMethod"></A>Experimental Method</td>
|
||
<td class="format1B" valign="Top">[EXP]<BR>[EXPM]</td>
|
||
<td class="format1B" valign="Top">The <A HREF="#DataTypeExperimentalMethods">experimental method</A> used to characterize the protein structure. Most structures are resolved using X-ray crystallography or nuclear magnetic resonance (NMR) but additional methods also exist (e.g., electron microscopy).<BR><BR>
|
||
To see the full list of experimental methods available, open the <A HREF="#SearchMethodAdvanced"><b>Advanced Search</b></A> page, select the ExpMethod search field in the <A HREF="#SearchBuilder">Search Builder</A> section, and press the <A HREF="#SearchMethodShowIndex">Show index</A> link to browse the index of available terms.<BR><BR>
|
||
<!-- {Questions: (A) The ExpMethod index lists three hits for "theoretical" (NOTE from Tom, 1/6/10: the PDB formatted file for one of the hits, 1VYC, includes the line "EXPDTA: Solution NMR; theoretical model", indicating that the data is indeed experiemental. However, the abstract of the associated publication refers to use of molecular dynamics, so maybe the authors applied that (theoretical) technique to the coordinates they got from NMR); (B) also The search results for:
|
||
<BR><BR>search #1: "electron microscopy"[exp]
|
||
<BR>search #2: "cryo electron microscopy"[exp]
|
||
<BR><BR>appear to be non-overlapping. Search #1 gets 124 hits, and search #2 gets 131 hits as of 07 Jan 2010. If you OR the results together, you get 255 hits, so the sets don't intersect at all.
|
||
<BR><BR>The puzzling part of this, however, is that some hits from search #1 say "Cryo-Em" in the docsum, and the PDB files of some hits retrieved by search #2 say "EXPDTA: electron microscopy" (rather than "EXPDTA: cryo electron microcopy"). So it's not clear why at least some of the records in the two data sets are indexed as they are.} -->
|
||
<!-- BR><BR>NOTE from Tom, 1/6/10: the PDB files for some sample records retrieved by searches 1 and 2 contain: "EXPDTA: electron microscopy". The phrase "cryo-em" appears in the docsum display of some of the hits from both searches, but we didn't see the pharse "cryo electron microscopy" in the EXPDTA line of any sample PDB files we opened.) --></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <a HREF="/sites/entrez?cmd=search&db=structure&term=x_ray[exp]&dopt=DocSum"><b>x_ray[exp]</b></a>      <I>or</I><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=%22x+ray%22[exp]&dopt=DocSum"><b>"x ray"[exp]</b></a><BR><BR>
|
||
will retrieve structures resolved by X-ray crystallography.<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=nmr[exp]&dopt=DocSum"><b>nmr[exp]</b></a><BR><BR>
|
||
will retrieve structures resolved by nuclear magnetic resonance.<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=%22electron+microscopy%22[exp]&dopt=DocSum"><b>"electron microscopy"[exp]</b></a><BR><BR>
|
||
will retrieve structures resolved by electron microscopy.
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldGeneDescription"></A>Gene Description</td>
|
||
<td class="format1B" valign="Top">[GDSC]<BR>[GeneDescription]</td>
|
||
<td class="format1B" valign="Top">The description of the gene that codes for a protein molecule present in the structure record.<BR><BR>
|
||
(The gene description is the text that is present in the "summary" section of the corresponding <A HREF="/gene/">Entrez Gene</A> record.)<BR><BR>
|
||
The association between the gene names and the protein molecules has been made using the <A HREF="#LinksGene">method</A> described under "<A HREF="#DocSumLinks">Find related data</A>."
|
||
<BR><BR></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&Term=%22tumor+suppressor%22%5BGDSC%5D"><b>"tumor suppressor"[GDSC]</b></a><BR><BR><!-- Use the escape character %22 in the URL to represent quotes around the phrase.<BR><BR -->
|
||
will retrieve structure records that contain the protein product of any gene that contains the term "tumor suppressor" in the gene's description.<BR><BR>
|
||
The <A HREF="#SearchTipsQuotes">quotes</A> surrounding the search terms ensure they are searched as a phrase.<A HREF="#SearchTipsQuotes">**</A> <!-- If quotes are not used and the terms are not automatically recognized as a phrase by the Entrez system, Entrez will insert a Boolean AND between the terms and they may or may not appear adjacent to each other in the retrieved records. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldGeneName"></A>Gene Name</td>
|
||
<td class="format1B" valign="Top">[GN]<BR>[GENE]<BR>[GNAME]<BR>[GeneName]</td>
|
||
<td class="format1B" valign="Top">The name of the gene that codes for a protein molecule present in the structure record.<BR><BR>
|
||
Because a gene may be known by a variety of names, this search field includes the official symbol<!-- , official full name, --> and the alternative ("also known as") gene symbols that are listed in the corresponding <A HREF="/gene/">Entrez Gene</A> record.<BR><BR>
|
||
For <B>example</B>, the Entrez Gene record for the <A HREF="/gene/7157"><B>human tumor protein p53</B></A> is known by the following names: <BR>
|
||
<B>Official Symbol: TP53</B><BR>
|
||
<!-- Official Full Name: tumor protein p53<BR -->
|
||
<B>Also known as: P53; LFS1; TRP53</B><BR><BR>
|
||
You can enter any of those terms in a search of the Gene Name field in order to retrieve structures that contain the protein product.<BR><BR>
|
||
The association between the gene names and the protein molecules has been made using the <A HREF="#LinksGene">method</A> described under "<A HREF="#DocSumLinks">Find related data</A>."
|
||
<BR><BR>
|
||
</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=TP53[GENE]&dopt=DocSum"><b>TP53[GENE]</b></a><BR><BR>
|
||
will retrieve structure records that contain the protein product of the TP53 (tumor protein p53) gene.
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldFilter"></A>Filter</td>
|
||
<td class="format1B" valign="Top">[FILT]</td>
|
||
<td class="format1B" valign="Top">The "Filter" search field allows you to narrow your retrieval to records that have certain attributes, such as <A HREF="#DataTypes">record type</A> (e.g., structures resolved using x-ray crystallography or NMR, which can also be retrieved via the <A HREF="#SearchFieldExpMethod">ExpMethod</A> field).<BR><BR>
|
||
The "Filter" field also allows you to limit search results to structure records that have links to other Entrez databases of interest, as shown in the sample search to the right. <!-- The latter attributes can also be specified by using the <a href="#DocSumDisplayMenu">"Display"</a> and <a href="#DocSumLinks">"Links"</a> menus of an <a href="#SearchResults">Entrez search results</a> page, and are also shown in the <a href="#BSSummaryFolderTabs">folder tabs</a> on a <a href="#SummaryPage">BioSystems Summary Page</a> for an individual record. --> A <a href="#DocSumLinks">detailed explanation of each type of link</a> is provided in the description of an Entrez <A HREF="#SearchResults">search results</A> page.<BR><BR>
|
||
The Filter field can also be used to view current database statistics, by entering a search for <I>All[Filt]</I>, as shown in the example in the next column.<BR><BR>
|
||
<!-- {Questions:
|
||
<BR><BR>(1) what subset of structure records do the Filter terms "complex dna," "complex ligand," "complex protein," and "complex rna" retrieve?
|
||
<BR><BR>(2) There is a difference of 70 records in number of hits when searching for x_ray[filt] 53,485 hits vs. x_ray[expmethod] 53,415 hits. However, the nmr[filt] and nmr[expmethod] searches work ok -- both retrieve 8,164 hits} --></td>
|
||
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=nmr[filt]&dopt=DocSum"><b>nmr[filt]</b></a><BR><BR>
|
||
will retrieve only that <A HREF="#DataTypes">record type</A> from the Structure database.<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=structure_pccompound[filt]&dopt=DocSum"><b>structure_pccompound[filt]</b></a><BR><BR>
|
||
will retrieve the structure records that have associated data (i.e., bound chemicals) in the <A HREF="/sites/entrez?db=pccompound">PubChem Compound</A> database.<BR><BR>
|
||
You can then open the "Display" menu near the top of the Structure search results page and select "Chemicals/<a href="#LinksPubChemCompound">PubChem Compound</a>" to retrieve the PubChem records for bound chemicals that are present in the structures you have retrieved, or only for those whose checkboxes have been activated. (Conversely, it is possible to <A HREF="mmdb_how_to_search_by_chemical.html">retrieve 3D structures that are bound to a specific chemical</A>.)<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=all[filt]&dopt=DocSum"><b>all[filt]</b></a><BR><BR>
|
||
will retrieve all of the structure database records, showing the total number retrieved. (Additional database statistics are available on the <A HREF="mmdb_news.html">news</A> page.)
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldJournal"></A>Journal</td>
|
||
<td class="format1B" valign="Top">[JOUR]</td>
|
||
<td class="format1B" valign="Top">The journal of the publication that reported the PDB structure findings. If more than one PubMed reference is associated with a structure record, the journal of each article has been indexed.
|
||
<BR><BR>
|
||
Journal names can be written as full names or abbreviations. To see the list of journals, open the <A HREF="#SearchMethodAdvanced"><b>Advanced Search</b></A> page, select the "Journal" search field in the <A HREF="#SearchBuilder">Search Builder</A> section, and press the <A HREF="#SearchMethodShowIndex">Show index</A> link to browse the index of available terms.<BR><BR>
|
||
</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=Science[jour]&dopt=DocSum"><b>Science[jour]</b></a><BR><BR>
|
||
will retrieve structures published in the journal <I>Science</I>.</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldMMDBEntryDate"></A>MMDB Entry Date</td>
|
||
<td class="format1B" valign="Top">[DDAT]</td>
|
||
<td class="format1B" valign="Top">The first date on which a particular MMDB ID appeared. This can represent the date on which a new Protein Data Bank structure record (i.e., a particular PDB accession) was <I>first <A HREF="#SourceDatabases">imported</A></I> into MMDB, or the date on which a previously existing PDB record was significantly changed and therefore received a new MMDB ID.
|
||
<BR><BR>
|
||
The syntax for searching the field is YYYY/MM/DD, YYYY/MM, or YYYY. The colon (:) can be used to search for a <A HREF="#SearchMethodRangeQuery">range</A> of dates, for example, YYYY/MM/DD<B>:</B>YYYY/MM/DD[MDAT]. <!-- (more about <A HREF="#SearchMethodRangeQuery">range searching</A>..) -->
|
||
<BR><BR>
|
||
Searches of this field will retrieve: (a) new structure records (PDB accessions) that were not previously in MMDB, and (b) PDB accessions that were previously in the database but that have changed in some significant way<!-- (such as re-ordering of atoms in a file as a result of a PDB remediation) --> and have therefore received a new MMDB ID. For example, if the atoms in a previously available PDB data file were re-ordered during a PDB remediation the PDB accession will remain the same but it will receive a new MMDB ID and a new MMDBEntryDate.
|
||
<BR><BR>
|
||
<!-- I>Note: Two structure records might have the same PDB accession but different MMDB IDs if something about the PDB record was changed significantly, for example, if the atoms in the record were re-ordered during a PDB remediation.</I -->
|
||
<!-- I>{Question: Should the database statistics for 2009[DDAT] and 2009[PDDAT] be roughly the same? Those searches retrieve 9033 and 4393, respectively, as of 12/16/09, which makes it appear that MMDB received twice as many new records as PDB did during the year. ANSWER: No, the stats are not necessarily the same. the 9033 hits include records with a PDDAT of 2009, plus records that had older PDDATs and were HUP'ed so just became publicly available in 2009, plus previously existing PDB accessions that received new MMDB IDs due to significant changes made during PDB remediation.}</I --></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2009[DDAT]&dopt=DocSum"><b>2009[DDAT]</b></a><BR><BR>
|
||
will retrieve structure records that were first imported into MMDB, or that have changed significantly, in the year 2009.<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2009/01[DDAT]&dopt=DocSum"><b>2009/01[DDAT]</b></a><BR><BR>
|
||
will retrieve new structure records that were first imported into MMDB, or that have changed significantly, in the month of January 2009.<BR><BR>
|
||
<a HREF="/sites/entrez?Db=structure&Cmd=DetailsSearch&Term=2009%2F01%2F10%5BDDAT%5D+%3A+2009%2F01%2F25%5BDDAT%5D&dopt=DocSum"><b>2009/01/10[DDAT] : 2009/01/25[DDAT]</b></a><BR><BR>
|
||
will retrieve new structure records that were first imported into MMDB, or that have changed significantly, anytime between January 10, 2009 and January 25, 2009.<BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I></td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldMMDBID"></A><A NAME="SearchFieldUID"></A>MMDB ID</td>
|
||
<td class="format1B" valign="Top">[MMDBID]<BR>[UID]<BR>[ID]</td>
|
||
<td class="format1B" valign="Top">The unique identifier (<!-- A HREF="#MmdbsrvMMDBID" -->MMDB ID) of the structure record in the <A HREF="/sites/entrez?db=structure">Molecular Modeling Database (MMDB)</A>. It is <!-- a string of digits --> an integer assigned consecutively to each structure record processed by NCBI. For example, <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885">50885</A> is the MMDB ID for sheep prostaglandin H2 synthase. (The <A HREF="#SummaryPage">summary page</A> for a structure record shows both of its <A HREF="#MmdbsrvRecordIdentifiers">identifiers</A>: <!-- A HREF="#MmdbsrvMMDBID" -->MMDB ID and corresponding <!-- A HREF="#MmdbsrvPDBID" -->PDB ID. The latter is searchable in the <A HREF="#SearchFieldPdbAcc">PDB Accession</A> field.)<BR><BR>
|
||
If you enter <!-- a string of digits --> an integer as a query and do not specify a search field, the MMDB ID field will be searched by default.<BR><BR>
|
||
<I>Note:</I> <!-- As mentioned in the section on <A HREF="#MmdbsrvRecordIdentifiers">structure record identifiers</A -->The <A HREF="#MmdbsrvMMDBID">MMDB ID</A> assigned to a <A HREF="#MmdbsrvPDBID">PDB accession</A> can change if there have been significant changes to the data in a record. For example, if the atoms in a previously available PDB data file were re-ordered during a PDB remediation the PDB accession will remain the same but it will receive a new MMDB ID and a new <A HREF="#SearchFieldMMDBEntryDate">MMDBEntryDate</A>. Obsolete MMDB IDs (e.g., 6543) cannot be retrieved through the <A HREF="/structure">Entrez Structure</A> search interface, even with direct searches of the UID field, because they are no longer indexed. However, those obsolete MMDB IDs can be retrieved from the archival copy of the database by using the "Direct Fetch via UID" option on the MMDB <A HREF="mmdb_search.html">Search Methods</A> page.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=50885[UID]&dopt=DocSum"><b>50885[UID]</b></a> <BR><BR>
|
||
will retrieve the structure record whose unique identification number is 50885.<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=50885&dopt=DocSum"><b>50885</b></a><BR><BR>
|
||
will also retrieve that same structure record, because the MMDB ID field is searched by default for queries that are only a string of digits<!-- an integer -->.
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldMMDBModifyDate"></A>MMDB Modify Date</td>
|
||
<td class="format1B" valign="Top">[MDAT]</td>
|
||
<td class="format1B" valign="Top">The date on which the structure record was last modified. If no modifications were made since the record was deposited into MMDB, then MMDBModifyDate will be the same as the <A HREF="#SearchFieldMMDBEntryDate">MMDBEntryDate</A>.<BR><BR>
|
||
<!-- I>{Question: Is it correct to say: Structure records that were imported for the first time will have the same MMDBEntryDate and MMDBModifyDate; if they are updated in the future, only their MMDBModifyDate will change. If yes, why does 2009/01[DDAT] retrieve 495 records and 2009/01[MDAT] retrieve only 184 as of 12/16/09?}</I><BR><BR -->
|
||
The syntax for searching the field is YYYY/MM/DD, YYYY/MM, or YYYY. The colon (:) can be used to search for a <A HREF="#SearchMethodRangeQuery">range</A> of dates, for example, YYYY/MM/DD<B>:</B>YYYY/MM/DD[MDAT]. <!-- (more about <A HREF="#SearchMethodRangeQuery">range searching</A>..) --><BR><BR>
|
||
<I>Note about this field:</I> When <B>PDB</B> undergoes a database <B>remediation</B>, in which most or all PDB records are updated in some way, MMDB imports the complete set of updated records. This was the case when the PDB database underwent a September 2007 remediation. Because the complete revised PDB data set was loaded into MMDB at that time, the earliest available value in the MMDBModifyDate field is 2007. Similarly, the release of PDB Archive Version 3.15 in March 2009 resulted in changes to a large subset of records, which is reflected in an MMDB MDAT of 2009/07 for approximately 20,000 records.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
The following searches will retrieve updated structure records that were previously in MMDB but that have changed in some way, as well as new structure records that became available during the specified period of time:<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2009[MDAT]&dopt=DocSum"><b>2009[MDAT]</b></a><BR><BR>
|
||
will retrieve the structure records that were updated and newly added to MMDB in the year 2009.<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2009/01[MDAT]&dopt=DocSum"><b>2009/01[MDAT]</b></a><BR><BR>
|
||
will retrieve the structure records that were updated and newly added to MMDB in the month of January 2009.<BR><BR>
|
||
<a HREF="/sites/entrez?Db=structure&Cmd=DetailsSearch&Term=2009%2F01%2F10%5BMDAT%5D+%3A+2009%2F01%2F25%5BMDAT%5D&dopt=DocSum"><b>2009/01/10[MDAT] : 2009/01/25[MDAT]</b></a><BR><BR>
|
||
will retrieve structure records that were updated and newly added to MMDB from January 10, 2009 through January 25, 2009.<BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldNumberOfPDBRecordsPerStructure"></A>Number of PDB Records per Structure</td>
|
||
<td class="format1B" align="center" valign="Top" colspan="3"><I>See <A HREF="#SearchFieldPdbFileCount">PDB File Count</A></I></td>
|
||
</tr>
|
||
|
||
<!-- DISCONTINUED SEARCH FIELD AS OF JUNE 2012 -->
|
||
<!-- tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldModDNAResCount"></A>ModDNAResCount</td>
|
||
<td class="format1B" valign="Top">[MDRC]<BR>[MDRCNT]<BR>[MDRCOUNT]</td>
|
||
<td class="format1B" valign="Top">The number of modified DNA residues in the PDB structure. This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  [FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________.]
|
||
</td>
|
||
</tr -->
|
||
|
||
|
||
<!-- DISCONTINUED SEARCH FIELD AS OF JUNE 2012 -->
|
||
<!-- tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldModProteinResCount"></A>ModProteinResCount</td>
|
||
<td class="format1B" valign="Top">[MPRC]<BR>[MPRCNT]<BR>[MPRCOUNT]</td>
|
||
<td class="format1B" valign="Top">The number of modified protein residues in the PDB structure. This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  [FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________.]
|
||
</td>
|
||
</tr -->
|
||
|
||
|
||
<!-- DISCONTINUED SEARCH FIELD AS OF JUNE 2012 -->
|
||
<!-- tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldModRNAResCount"></A>ModRNAResCount</td>
|
||
<td class="format1B" valign="Top">[MRRC]<BR>[MRRCNT]<BR>[MRRCOUNT]</td>
|
||
<td class="format1B" valign="Top">The number of modified RNA residues in the PDB structure. This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  [FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________.]
|
||
</td>
|
||
</tr -->
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldOligomericState"></A>Oligomeric State</td>
|
||
<td class="format1B" valign="Top">[OL]<BR>[OS]<BR>[OLIG]<BR>[OligomericState]</td>
|
||
<td class="format1B" valign="Top">A term representing the number of biopolymers (i.e., protein and nucleotide (RNA/DNA) molecule) in the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A>.<BR><BR>
|
||
For example, this search field contains terms such as:<BR><BR>
|
||
monomeric<BR>
|
||
dimeric<BR>
|
||
trimeric<BR>
|
||
tetrameric<BR>
|
||
pentameric<BR>
|
||
hexameric<BR>
|
||
octomeric<BR>
|
||
 9-meric<BR>
|
||
10-meric<BR>
|
||
...<BR>
|
||
23-meric<BR>
|
||
...<BR>
|
||
60-meric<BR><BR>
|
||
|
||
As noted in the section of this document that describes the <A HREF="#DataProcessingBiologicalFormsProcedures">procedures used to identify the biological unit</A>, the oligomeric state is derived from the "<B>REMARK 350</B>" record of the <B>PDB source file</B>. <I>(The documentation about <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A> provides more information about the various "records" (data fields) that are present in PDB source files.)</I><BR><BR>
|
||
Also note that the oligomeric state of a structure might reflect its bound state. For example, the PDB source file for <A HREF="/Structure/pdb/1TUP">1TUP</A>: "Tumor Suppressor P53 Complexed With DNA" defines the oligomeric state as pentameric (a trimer protein complexed with a DNA double helix).
|
||
</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldOrganism"></A>Organism</td>
|
||
<td class="format1B" valign="Top">[ORGN]</td>
|
||
<td class="format1B" valign="Top">The source organism(s) of the <A HREF="#MmdbsrvMolecularComponents">protein and/or nucleotide molecules</A> in the structure record. A common name (e.g., human), scientific name (e.g., <I>Homo sapiens</I>), or other taxonomic node (e.g, Primates or Primata) can be entered as a query.<BR><BR>
|
||
If a structure record contains protein or nucleotide sequences from more than one organism (e.g., <A HREF="/sites/entrez?cmd=search&db=structure&term=%22human%22%5BOrganism%5D+AND+HIV1%5BOrganism%5D&dopt=DocSum"><I>human AND HIV1</I></A>), the record can be retrieved by searching for any one of the source organisms.<BR><BR>
|
||
The <A HREF="#SummaryPage">summary page</A> for an individual structure provides a list of the <A HREF="#MmdbsrvTaxonomy">source organism(s)</A>. Each organism name links to the corresponding taxonomic information in the <A HREF="/sites/entrez?db=taxonomy">NCBI Taxonomy database</A>, including the organism's Taxonomy ID (<A HREF="/books/NBK21100/#A268">TaxID</A>) and lineage. <!-- For additional information, see the <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A><A HREF="#DataProcessingDirectLinksTaxonomy"><B>taxonomy</B></A> section of this document. --></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=human[orgn]&dopt=DocSum"><b>human[orgn]</b></a><BR><BR>
|
||
will retrieve structures with at least one <A HREF="#MmdbsrvMolecularComponents">molecular component</A> from human.<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=primates[orgn]&dopt=DocSum"><b>primates[orgn]</b></a><BR><BR>
|
||
will retrieve structures with at least one <A HREF="#MmdbsrvMolecularComponents">molecular component</A> from any species falling in the order Primata.
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldOtherMoleculeName"></A>Other Molecule Name</td>
|
||
<td class="format1B" valign="Top">[ONAM]<BR>[ONAME]<BR>[OtherMoleculeName]</td>
|
||
<td class="format1B" valign="Top">The name of a molecule -- other than a protein, DNA, RNA, or ligand -- that is present in a structure record. The name is derived from the COMPND record of the PDB source file and represents the term used by the author for the molecule.<BR><BR>
|
||
(The documentation about <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A> provides more information about the various "records" (data fields) that are present in PDB source files.)</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
 <!-- a HREF="/sites/entrez?cmd=search&db=structure&term=arabino+nucleic+acids[ONAM]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldPdbAccession"></A><A NAME="SearchFieldPdbAcc"></A>PDB Accession</td>
|
||
<td class="format1B" valign="Top">[ACCN]<BR>[PACC]<BR>[PDBACC]</td>
|
||
|
||
<td class="format1B" valign="Top">The accession of number of the <A HREF="http://www.rcsb.org/pdb/">Protein Data Bank (PDB)</A> record from which the MMDB record was derived, and is sometimes referred to as PDB ID. It is generally a four-character alphanumeric combination (e.g., <A HREF="http://www.rcsb.org/pdb/explore/explore.do?pdbId=1PTH">1PTH</A> is the source record for MMDB ID <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885">50885</A>).<BR><BR>
|
||
The PDB ID shown on an MMDB <A HREF="#SearchResults">search results page</A> opens the corresponding MMDB <A HREF="#SummaryPage">structure summary page</A>.
|
||
The PDB ID on the structure summary page, in turn, links to the source record on the PDB web site.<BR><BR>
|
||
The <A HREF="#MmdbsrvRecordIdentifiers">record identifiers</A> section of a <A HREF="#SummaryPage">structure summary page</A> also lists the corresponding <!-- A HREF="#MmdbsrvMMDBID" -->MMDB ID, which is searchable in the <A HREF="#SearchFieldUID">UID</A> field.<BR><BR></td>
|
||
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=1PTH[pdbacc]&dopt=DocSum"><b>1PTH[pdbacc]</b></a><BR><BR>
|
||
will retrieve the MMDB record for 1PTH, for sheep prostaglandin H2 synthase.</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldPDBChemicalCode"></A><A NAME="SearchFieldLigCode"></A>PDB Chemical Code</td>
|
||
<td class="format1B" valign="Top">[LigCode]<BR>[LCOD]<BR>[LIGC]<BR>[LCODE]</td>
|
||
<td class="format1B" valign="Top">The 3-letter code of a ligand (bound chemical) in the PDB structure. For example, HEM is the ligand code for a heme group in a globin.
|
||
<!-- BR><BR>{Question: assigned by PDB? Any caveats in using this field?} -->
|
||
<BR><BR>
|
||
A separate file shows how to <A HREF="mmdb_how_to_search_by_chemical.html">find 3D structures bound to a specific chemical (e.g., aspirin)</A>.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<!-- DISCONTINUED SEARCH FIELD AS OF JUNE 2012 -->
|
||
<!-- tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldPdbChainCode"></A>PDBChainCode</td>
|
||
<td class="format1B" valign="Top">[CHN]<BR>[CHNC]<BR>[CCODE]</td>
|
||
<td class="format1B" valign="Top">The 1-letter PDB chain code for a protein or nucleotide chain (i.e., a protein or nucleotide molecule).<BR><BR>
|
||
For example, the structure of the <B>P53 tumor suppressor</B> (accession <A HREF="/Structure/pdb/1TUP">1TUP</A>) includes three protein molecules (with the PDB chain codes A, B, and C) and two nucleotide molecules (with the PDB chain codes E and F).<BR><BR>
|
||
{{Question: Is this field case sensitive? Why would someone use this field -- e.g., perhaps to retrieve records with certain numbers of chains -- e.g., if user searches for <I>a[CHN]</I>, they will presumably get records containing 27 chains (upper case A-Z, and lower case A)?}{
|
||
</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  [FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________.]
|
||
</td>
|
||
</tr -->
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldPdbClass"></A>PDB Class</td>
|
||
<td class="format1B" valign="Top">[PCLA]<BR>[PCLS]</td>
|
||
<td class="format1B" valign="Top">The classification of the PDB structure, as provided by the submitter in their data file.<BR><BR>
|
||
<!-- {Question: using what classification scheme -- e.g., SCOP? GO? other?} --></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldPdbComment"></A>PDB Comment</td>
|
||
<td class="format1B" valign="Top">[PCOM]<BR>[PCMT]</td>
|
||
<td class="format1B" valign="Top">The more detailed description of the PDB structure. This field contains text from the REMARK records in the PDB data file.<BR><BR>
|
||
<!-- {Question: provided by the author? by PDB? Extracted from which line of the PDB record?} --></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldPDBDepositDate"></A>PDB Deposit Date</td>
|
||
<td class="format1B" valign="Top">[PDDAT]</td>
|
||
<td class="format1B" valign="Top">The <I>earliest date</I> that Protein Data Bank associates with an accession, generally representing the date on which the record was submitted to the PDB.<BR><BR>
|
||
The syntax for searching the field is YYYY/MM/DD, YYYY/MM, or YYYY. The colon (:) can be used to search for a <A HREF="#SearchMethodRangeQuery">range</A> of dates, for example, YYYY/MM/DD<B>:</B>YYYY/MM/DD[MDAT]. <!-- (more about <A HREF="#SearchMethodRangeQuery">range searching</A>..) --><BR><BR>
|
||
<I>(Note that the PDB Deposit Date is not necessarily the date on which the record became publicly available, and may be significantly different from the release date if submitters requested their data remain confidential until publication.)</I></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2009[PDDAT]&dopt=DocSum"><b>2009[PDDAT]</b></a><BR><BR>
|
||
will retrieve the structure records that were submitted to PDB in the year 2009.<BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=2009/01[PDDAT]&dopt=DocSum"><b>2009/01[PDDAT]</b></a><BR><BR>
|
||
will retrieve the structure records that were submitted to PDB in January 2009.<BR><BR>
|
||
<a HREF="/sites/entrez?Db=structure&Cmd=DetailsSearch&Term=2009%2F01%2F10%5BPDDAT%5D+%3A+2009%2F01%2F25%5BPDDAT%5D&dopt=DocSum"><b>2009/01/10[PDDAT] : 2009/01/25[PDDAT]</b></a><BR><BR>
|
||
will retrieve structure records that were submitted to PDB anytime between January 10, 2009 and January 25, 2009.<BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldPdbDescription"></A><A NAME="SearchFieldPdbDescr"></A>PDB Description</td>
|
||
<td class="format1B" valign="Top">[PDSC]<BR>[PDES]</td>
|
||
<td class="format1B" valign="Top">A brief description of the PDB structure.<BR><BR> <!-- {Question: Provided by the author? Extracted from which line of the PDB record?} --></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldPdbFileCount"></A>PDB File Count<BR><BR><I>(Number of PDB records per structure)</I></td>
|
||
<td class="format1B" valign="Top">[PdbFileCount]<BR>[FC]<BR>[PDBCNT]</td>
|
||
<td class="format1B" valign="Top">The number of PDB records that have been combined to reconstitute the originally submitted structure.<BR><BR>
|
||
Most structures occupy a single PDB record.<BR><BR>
|
||
Very large structures have been split by PDB into multiple records, and the MMDB data processing procedures <A HREF="#DataProcessingMergeSplitFiles"><B>merge the PDB split</B></A> files back into a single structure record.<BR><BR>
|
||
</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<A HREF="/sites/entrez?db=structure&Cmd=search&term=2%5BPdbFileCount%5D+%3A+1000%5BPdbFileCount%5D"><B>2[FC] : 1000[FC]</B></A><BR><BR>
|
||
will retrieve all structures that have a PDB file count of 2 or more (in this search example, the upper limit was arbitrarily set at 1000).<BR><BR>
|
||
In other words, the search will <A HREF="/sites/entrez?db=structure&Cmd=search&term=2%5BPdbFileCount%5D+%3A+1000%5BPdbFileCount%5D">retrieve all merged files</A> from MMDB.
|
||
<!-- the search will retrieve all <A HREF="#DataProcessingMergeSplitFiles">merged files</A> from MMDB. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldPdbSource"></A>PDB Source</td>
|
||
<td class="format1B" valign="Top">[PSRC]<BR>[PSOU]</td>
|
||
<td class="format1B" valign="Top">The source organism of each protein and/or nucleotide molecule, as noted in the original PDB data file.
|
||
<BR><BR>
|
||
<I>Note: During MMDB data processing, the source organism names in the PDB data file are compared against the organism names in the <A HREF="/taxonomy/">NCBI Taxonomy database</A>. If there is a difference, the MMDB version of the data file will contain the organism name from the NCBI taxonomy database (based on the results of a <A HREF="https://blast.ncbi.nlm.nih.gov/Blast.cgi">BLAST</A> search), and that name will be searchable in the <A HREF="#SearchFieldOrganism">Organism</A> field. However, the source organism name noted in the original PDB file will still also be searchable via the PDBSource field.</I>
|
||
<BR><BR>
|
||
<!-- {Question: the source organism of each protein and/or nucleotide molecule, as noted in the original PDB record (before MMDB data processing step that assigns organism name(s) from Taxonomy database)?} --></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldProteinName"></A>Protein Name</td>
|
||
<td class="format1B" valign="Top">[PNAM]<BR>[PNAME]<BR>[ProteinName]</td>
|
||
<td class="format1B" valign="Top">The name of a protein molecule in a structure record, derived from the COMPND record of the PDB source file. This represents the term used by the author for the protein.<BR><BR>
|
||
(The documentation about <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A> provides more information about the various "records" (data fields) that are present in PDB source files.)</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldResolution"></A>Resolution</td>
|
||
<td class="format1B" valign="Top">[RES]<BR>[RESL]<BR>[RESO]</td>
|
||
<td class="format1B" valign="Top">The resolution (in Angstroms) of a protein structure resolved by diffraction or electron microscopy. This field can be queried for a single value or a <A HREF="#SearchMethodRangeQuery">range of values</A>.<BR><BR>
|
||
<!-- {Question: where in the record does the resolution value exist -- in what field of PDB data file? is it shown in the structure summary page? Is there a way to check if the results retrieved indeed match the query?} --></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<A HREF="/sites/entrez?db=structure&cmd=search&term=001.50%5BResolution%5D+%3A+001.75%5BResolution%5D&dopt=DocSum"><B>001.50 : 001.75[Resolution]</B></A><BR><BR>
|
||
will retrieve records that have a resolution between 1.50 to 1.75 Angstroms.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>001.50[Resolution] : 001.75[Resolution]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldRNAName"></A>RNA Name</td>
|
||
<td class="format1B" valign="Top">[RNAM]<BR>[RNAME]<BR>[RNAName]</td>
|
||
<td class="format1B" valign="Top">The name of an RNA molecule in a structure record. The names of nucleotide molecules, including DNA and RNA, are derived from the COMPND record of the PDB source file.<BR><BR>
|
||
(The documentation about <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A> provides more information about the various "records" (data fields) that are present in PDB source files.)<BR><BR>
|
||
The RNA name often reflects the sequence of nucleotides in the molecule itself.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  <!-- FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________. -->
|
||
</td>
|
||
</tr>
|
||
|
||
|
||
<tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchFieldTitle"></A>Title</td>
|
||
<td class="format1B" valign="Top">[Title]<BR>[TITL]</td>
|
||
<td class="format1B" valign="Top">The title of the publication(s) that reported the PDB structure findings. If more than one PubMed reference is associated with a structure record, the title of each article has been indexed.<BR><BR>
|
||
<!-- {Question: If more than one PubMed reference is associated with a structure record, will the title of each article be indexed, or will only the title of the primary reference (listed on the structure summary page) be indexed?} --></td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=%22p53+tumor+suppressor%22[TITL]&dopt=DocSum"><b>"p53 tumor suppressor"[TITL]</b></a><BR><BR>
|
||
will retrieve structure records with that phrase in the title.<BR><BR>
|
||
<I>(Compare these search results with those obtained by the sample <A HREF="#SearchFieldAll">All Fields</A> search, which will retrieve structure records containing that phrase anywhere in the record, and those obtained by the sample <A HREF="#SearchFieldAbstract">Citation Abstract Field</A> search, which will retrieve structure records containing that phrase in the abstract of an associated PubMed record.)</I><BR><BR>
|
||
The <A HREF="#SearchTipsQuotes">quotes</A> surrounding the search terms ensure they are searched as a phrase.<A HREF="#SearchTipsQuotes">**</A></td>
|
||
</tr>
|
||
|
||
|
||
<!-- TEMPLATE WITH ARROW_UP IN LAST CELL -->
|
||
<!-- tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchField__________"></A>__________</td>
|
||
<td class="format1B" valign="Top">[____]<BR>[____]<BR>[____]</td>
|
||
<td class="format1B" valign="Top">_______Description________</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
  [FINISH THIS <a HREF="/sites/entrez?cmd=search&db=structure&term=___[___]&dopt=DocSum"><b>___[___]</b></a><BR><BR>
|
||
will retrieve __________.]
|
||
</td>
|
||
</tr -->
|
||
|
||
|
||
<!-- TEMPLATE WITH ARROW_UP IN LAST CELL AND RANGE SEARCHING -->
|
||
<!-- tr>
|
||
<td class="format1A" valign="Top"><A NAME="SearchField_____"></A>________</td>
|
||
<td class="format1B" valign="Top">[____]<BR>[____]<BR>[____]</td>
|
||
<td class="format1B" valign="Top">_______Description________.</td>
|
||
<td class="format1B" valign="Top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
<A HREF="#SearchFields"><img SRC="../../IMG/buttons/toc_icon.png" width="15" height="12" border="0" align="right" alt="List of MMDB Search Fields"></A>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BPMC%5D&dopt=DocSum"><b>4 : 6 [PMC]</b></a>     <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4%5BPMC%5D+%3A+6%5BPMC%5D&dopt=DocSum"><b>4[PMC] : 6[PMC]</b></a>    <I>or</I><BR><BR>
|
||
<a HREF="/sites/entrez?cmd=search&db=structure&term=4+%3A+6%5BProteinMoleculeCount%5D&dopt=DocSum"><b>4 : 6[ProteinMoleculeCount]</b></a>    <BR><BR>
|
||
<I>etc.</I><BR><BR>
|
||
will retrieve structure records that contain anywhere from four to six protein molecules in the <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("biounit") of the structure.<BR><BR>
|
||
As you can see by clicking on the <A HREF="#SearchDetails">Details</A> folder tab after doing the search, each query above is translated to:<BR><BR>
|
||
<I>4[ProteinMoleculeCount] : 6[ProteinMoleculeCount]</I><BR><BR>
|
||
<I>(more about <A HREF="#SearchMethodRangeQuery">range searching</A>...)</I><BR><BR>
|
||
</td>
|
||
</tr -->
|
||
|
||
</table>
|
||
<BR>
|
||
|
||
<A NAME="SearchFieldTips"></A>
|
||
<A NAME="SearchFieldAbbreviations"></A>
|
||
* In a query, the <B>field name may be typed as the <A HREF="#SearchFields">full name or abbreviation</A></B>, and may be in upper, lower, or mixed case. If more than one abbreviation is shown, any one of them can be used. The field name must be surrounded by <B>square brackets []</B>. A space between the search term and the field specifier is optional. If desired, surround a phrase with <A HREF="#SearchTipsQuotes">quotes</A> to force an adjacency search. For example, the sample queries below will work equally:<BR>
|
||
      "p53 tumor suppressor"[TI] <BR>
|
||
      "p53 tumor suppressor"[TITL] <BR>
|
||
      "p53 tumor suppressor" [TITL] <BR>
|
||
      "p53 tumor suppressor" [titl] <BR>
|
||
      "p53 tumor suppressor"[Title] <BR><BR>
|
||
|
||
<A NAME="SearchTipsQuotes"></A>
|
||
** The <B>quotes surrounding the query terms</B> in some of the sample searches force the terms to be searched as a phrase. <B>If quotes are not used</B>, the <A HREF="/sites/gquery">Entrez</A> system may still recognize and handle the terms as a phrase, if they are present in a phrase dictionary used by the search engine. If the terms are <I>not</I> present in the phrase dictionary and are <I>not</I> surrounded by quotes, Entrez will insert a Boolean AND between the terms; in that case, they may or may not appear adjacent to each other in the retrieved records. The "<B>Details</B>" folder tab on a search results page will show you exactly how the Entrez system parsed your query. More search tips are provided in the <a HREF="/books/NBK3827/">PubMed help document</a> and <a HREF="/books/NBK3837/">Entrez help document</a>.<BR><BR>
|
||
|
||
<A NAME="SearchTipsTruncation"></A>
|
||
It is also possible to search for a word stem by using an <B>asterisk (*) as a wild card</B>; for example, inhibit* will retrieve records with terms such as inhibit, inhibited, inhibition, inhibitor, etc. The <A HREF="/books/NBK3837/">Entrez Help</A> document provides additional information about <A HREF="/books/NBK3837/#EntrezHelp.Using_Wild_Cards_or_Query_Tru">truncating</A> search terms in this way.
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ======== END_TABLE_OF_SEARCH_FIELDS_ABBREVIATIONS_DESCRIPTIONS ========= -->
|
||
|
||
<!-- ============= LEVEL_1_LINK_FROM_OTHER_DATABASE ============== -->
|
||
|
||
<A NAME="LinkFromOtherDatabase"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Link from other Entrez Database</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<A NAME="______"></A>
|
||
|
||
The <A HREF="/sites/gquery">Entrez</A> databases to which structure records have been linked (via the <A HREF="#DataProcessing">data processing</a> pipeline) generally have reciprocal links from their records back to the corresponding <A HREF="/sites/entrez?db=structure">Structure</A> database records.<BR><BR>
|
||
|
||
Therefore, if you start your search in an <A HREF="/sites/gquery">Entrez</A> database other than <A HREF="/sites/entrez?db=structure">Structure</A>, you can view the "<B>Related Information</B>" <!-- (formerly called "Links") -->menu in the right hand margin of any record you have retrieved to see if it has links to associated information in the Structure database, as shown in the <span style="color:#d70000">illustrated example</span> below.<BR><BR>
|
||
|
||
<!-- ILLUSTRATION OF PROTEIN SEQUENCE > RELATED STRUCTURES -->
|
||
|
||
<A NAME="LinkFromOtherDatabaseIllustration"></A>
|
||
<A HREF="https://structure.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi?query_gi=463989"><img src="../../cblast/docs/images/gi463989_dna_mismatch_repair_homolog_human_PROTEIN_SEQUENCE_and_RELATED_STRUCTURES.png" width="760" height="260" style="border: 0px; margin-top: 5px; margin-bottom: 5px;" alt="Illustration showing how to link from protein sequence record to related structures, using protein sequence GI 463989 as an exmaple, human DNA mismatch repair protein homolog. Click on the image to open the live Related Structures search results page."></A><br><br>
|
||
|
||
<!-- END ILLUSTRATION OF PROTEIN SEQUENCE > RELATED STRUCTURES -->
|
||
|
||
|
||
Additional, more detailed <span style="color:#d70000">illustrated examples</span> show how to link from a <A HREF="mmdb_how_to_search_by_gene.html">gene record or protein sequence to "related structures"</A>, and from a <A HREF="mmdb_how_to_search_by_chemical.html">PubChem record to "protein structures"</A> that are bound to the chemical of interest.<BR><BR>
|
||
|
||
Alternatively, you can use the "<B>Find Related Data</B>" menu in the right hand margin of an Entrez <I>search results page</I> (in whatever database you have chosen to search) and select "Structure" to view the associated structure records for all items (default) displayed on the search results page or for those you have selected using their checkboxes.<BR><BR>
|
||
|
||
<A NAME="LinksFromProteinToStructure"></A>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="black 1px" cellpadding="4" class="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD class="format1H" align="left">Additional note about links from <A HREF="/protein/"><B>Entrez Protein</B></A> <B>sequence records</B> to structure records: </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<!-- TD class="format1H" valign="top" width="180" style="white-space: nowrap;"><A NAME="_____"><B>Summary</B></A></TD -->
|
||
<TD class="format1B" valign="top">
|
||
|
||
<BR>Protein sequence records can have a link to 3D structure record depending upon the data available for a particular protein sequence:
|
||
|
||
<UL>
|
||
|
||
<LI><B>Structure</B> - <I>Protein sequence records that have a direct association with the structure record</I> because at least one of the following is true: (a) the protein sequence record was derived directly from a 3D structure record (as described in MMDB <A HREF="#DataProcessingDeposition">data processing</A>); (b) the accession number of the protein sequence record was listed in the DBREF record of the PDB source file; (c) the protein accession listed in the DBREF record of the PDB source file is also found in an Entrez Gene record, and that Gene record also has links to other protein accession(s); in such a case, all of the protein accessions in the Entrez Gene record will have "Structure" links (and will show a thumbnail image of a corresponding 3D structure in their protein sequence record display); or (d) the protein is identical in composition and sequence length to any of the proteins noted in (a), (b), or (c).<!-- NOTE: Part (d) is true for all protein sequences EXCEPT patent records. Patent sequences and environmental sequences are numerous but infrequently used, so they are not included in PIGs, PIGpen. --></LI><BR>
|
||
|
||
<!--<LI><B>Related Structures</B> - <I>Protein sequences from experimentally resolved 3D structures that are related to the query protein</I>, based on sequence similarity. Those are referred to as "related structures" and were identified by the <A HREF="../mmdb.shtml#CBLAST"><B>Related Structures (CBLAST)</B></A> service. The related structures might align to the full length of the query sequence, or only to a portion of it, and the CBLAST results page provides a graphical display that summarizes the extent of each match.<BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><B>Related Structures (List)</B> - Opens an <A HREF="/structure/">Molecular Modeling Database (MMDB)</A> display that lists the experimentally resolved 3D structure records that contain one or more protein molecules similar in sequence to the current protein(s). Each 3D structure and its corresponding sequence data can be viewed interactively in the free <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> web-based 3D viewer or the free <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> stand-alone software program.</LI><BR>
|
||
|
||
<LI><B>Related Structures (Summary)</B> - Opens a <A HREF="../mmdb.shtml#CBLAST">Related Structures (CBLAST)</A> graphical summary that: (a) lists the individual proteins from experimentally resolved 3D structures that are related to the query protein, based on sequence similarity, and (b) shows alignment footprints (as pink bars) that indicate regions of similarity between the query protein and the structure-based protein, with an option to view the 3D structure and corresponding sequence alignment interactively in the free <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A> web-based 3D viewer or the free <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> stand-alone software program.</LI><BR>
|
||
|
||
</UL>
|
||
|
||
See frames B and C of an <A HREF="mmdb_how_to_search_by_gene.html"><span style="color:#d70000">illustrated example</span></A> to see the "Related Structures" links that appear in the right hand margin of protein sequence record displays.</LI><BR>-->
|
||
</UL>
|
||
|
||
As of February 2020, approximately <B>0.6%</B> <!-- [455466 out of 824753812] --> of the 800+ million sequence records in <A HREF="/protein/"><B>Entrez Protein</B></A> have a direct "<B>Structure</B>" link, because they were derived from 3D structure records or have another type of direct association with a 3D structure. <!--However, approximately <B>51%</B> [42081946 out of 824753812, as of 02/12/2020] of the total protein sequence records have a "<B>Related Structures</B>" link.<BR><BR>-->
|
||
|
||
<!--If the "<B>Related Information</B>" (formerly called "Links") menu for an individual protein sequence record <B>does not contain</B> an option for "<B>Related Structures</B>", then no structure-based protein sequences were similar enough to your protein of interest to pass the <A HREF="../mmdb.shtml#CBLAST">CBLAST</A> score cutoff. However, other records in your protein search results might have a "Related Structures" link. Alternatively,--> You can <A HREF="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&DATABASE=pdb"><B>BLAST the protein sequence against the PDB (structure) database</B></A> and adjust the algorithm parameters to decrease the stringency of the search, if desired.<BR><BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
|
||
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_4_CONTENTS ====== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_4_CONTENTS ############ -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ############# BLUE_HEADER_SECTION_5_OUTPUT_SEARCH_RESULTS ############## -->
|
||
|
||
<A NAME="SearchResults"></A>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Search Results</SPAN></TD>
|
||
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ########### END_BLUE_HEADER_SECTION_5_OUTPUT_SEARCH_RESULTS ############ -->
|
||
|
||
|
||
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_5_CONTENTS ########### -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
||
<TR>
|
||
<TD class="WhiteCellBlueEdgeAll">
|
||
|
||
<!-- ============ MINI_TOC FOR SEARCH RESULTS ============== -->
|
||
<BR>
|
||
<BLOCKQUOTE><BLOCKQUOTE>
|
||
|
||
| <A HREF="#DocSumPage">document summary page</A> | <!-- A HREF="#DocSumShowSortbySendtoMenus">"display, show, sort by, send to" menus</A --><A HREF="#DocSumDisplayOptions">display settings</A>: <A HREF="#DocSumFormat">format</A>, <A HREF="#DocSumShow">items per page</A>, <A HREF="#DocSumSort">sort by</A> | <A HREF="#DocSumSendTo">send to</A> | <A HREF="#Filters">filter your results</A> | <A HREF="#SelectedRecords">refine your results</A> | <A HREF="#DocSumLinks">find related data</A> |
|
||
|
||
</BLOCKQUOTE></BLOCKQUOTE>
|
||
|
||
<!-- ========== END_MINI_TOC FOR SEARCH RESULTS ============ -->
|
||
|
||
<!-- ============== BEGIN_LEVEL_1_DOCSUM_PAGE_SECTION_HEADER ================ -->
|
||
<A NAME="DocSumPage"></A>
|
||
|
||
<!-- BR -->
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Document Summary (DocSum) page</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<!-- ============== BEGIN_LEVEL_1_DOCSUM_PAGE_INTRO ================ -->
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
|
||
The initial search results provide a list (<B>document summary</B>, or "<B>docsum</B>") of the structure records that contain your <A HREF="#SearchTips"><b>search term</b></A>, which <b>can appear in any field of the record</b>, unless a <A HREF="#SearchFields">search field</A> was specified in the query.
|
||
|
||
If desired, you can <b>narrow your search</b> by restricting the query to a </A><A HREF="#SearchFields">search field</A> of interest or adding more terms with a Boolean AND.
|
||
|
||
Alternatively, you can <b>broaden your search</b> by adding more terms (e.g., synonyms) to your query with a Boolean OR<!--, or by following links to <A HREF="#LinksSimilarStructures">Similar Structures</A-->.<BR><BR>
|
||
|
||
Once you are satisfied with your search results, click on the thumbnail image, <A HREF="#SearchFieldPdbAcc">PDB Accession</A>, or <A HREF="#SearchFieldUID">MMDB ID</A> of any record on the DocSum page to view its <A HREF="#SummaryPage">structure summary page</A>. <!-- I>(The PDB ID on the <A HREF="#SummaryPage">structure summary page</A> links to the source record on the PDB web site.)</I --> In addition, the following options are available for viewing the search results:<BR><BR>
|
||
|
||
<!-- | <A HREF="#DocSumDisplayMenu">Display</A> | <A HREF="#DocSumShow">Show</A> | <A HREF="#DocSumSort">Sort By</A> | <A HREF="#DocSumSendTo">Send To</A> | <A HREF="#DocSumLinks">Links</A> |
|
||
<BR><BR -->
|
||
</P>
|
||
|
||
<!-- ============== END_LEVEL_1_DOCSUM_PAGE_INTRO ================ -->
|
||
|
||
|
||
<!-- ==== TABLE_WITH_SAMPLE_STRUCTURE_SEARCH_RESULTS_DOCSUM_AND_MINI_TOC ==== -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD width="15"> </TD>
|
||
|
||
<!-- ======= IMAGE_SAMPLE_STRUCTURE_SEARCH_RESULTS_DOCSUM ======== -->
|
||
|
||
<TD width="650" ALIGN="LEFT" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
||
<TR>
|
||
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#SummaryPage"><A HREF="/sites/entrez?cmd=search&db=structure&term=%22prostaglandin+H2+synthase%22&dopt=DocSum">SAMPLE SEARCH RESULTS DISPLAY</A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="WhiteCellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<TR>
|
||
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="WhiteCell">
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=%22prostaglandin+H2+synthase%22&dopt=DocSum"><IMG src="images/1PTH_docsum_page.png" width="635" height="510" border=0 align="center" alt="Image of sample structure search results page for prostaglanin H2 synthase, with the search terms in quotes to force a phrase search. The READ MORE ABOUT column to the right of the image provides more details about the options on the search results page. Click on the image to open the live search results page in MMDB. Note that a larger number of items may be retrieved if new structures were deposited since this snapshot was taken."></A>
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</TD>
|
||
|
||
<!-- ========================== SPACER_CELL ================================= -->
|
||
|
||
<TD width="15"> </TD>
|
||
|
||
|
||
<!-- ======= MINI_TABLE_OF_CONTENTS_FOR_SEARCH_RESULTS_DOCSUM ========== -->
|
||
|
||
<TD ALIGN="LEFT" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
||
<TR>
|
||
<TD ALIGN="CENTER" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;">READ MORE ABOUT:</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="WhiteCellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" class="WhiteCell">
|
||
|
||
<UL style="list-style-type: disc;padding:0px; margin:20px;">
|
||
|
||
<LI><A HREF="#SearchMethodLimits"><B>Limits</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<LI><A HREF="#SearchMethodAdvanced"><B>Advanced Search</B></A>
|
||
<BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR>
|
||
</LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#SearchBuilder">Search Builder</A></LI>
|
||
<LI><A HREF="#SearchMethodShowIndex">Show Index</A></LI>
|
||
<!-- LI><A HREF="#SearchMethodPreview">Preview</A></LI -->
|
||
<LI><A HREF="#SearchMethodHistory">History</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#DocSumDisplayOptions"><B>Display Settings</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#DocSumFormat">Format</A></LI>
|
||
<LI><A HREF="#DocSumShow">Items per page</A></LI>
|
||
<LI><A HREF="#DocSumSort">Sort by</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#DocSumSendTo">"<B>Send To</B>" menu</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<LI><A HREF="#SearchResultsSubsets"><B>Subsets of Results</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#Filters">Filter your results</A></LI>
|
||
<LI><A HREF="#SelectedRecords">Refine your results</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#DocSumLinks"><B>Find Related Data</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#LinksSimilarStructures">Similar Structures</A></LI>
|
||
<LI><A HREF="#LinksLiterature">Literature</A></LI>
|
||
<LI><A HREF="#LinksSequences">Sequences</A></LI>
|
||
<LI><A HREF="#LinksDomains">Domains</A></LI>
|
||
<LI><A HREF="#LinksChemicals">Chemicals</A></LI>
|
||
<LI><A HREF="#LinksOther">Other Links</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#SearchDetails"><B>Search Details</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<LI>See <A HREF="/books/NBK3842/"><B><I>My NCBI help</I></B></A><!-- A HREF="/books/NBK3827/"><B><I>PubMed help</I></B></A --> for:<BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="/books/NBK53592/"><I>Save Search</I></A></LI>
|
||
<LI><A HREF="/books/NBK53590/"><I>Save Results</I></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0">
|
||
|
||
<!-- img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#_______">__________</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#_______">__________</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR>
|
||
|
||
- <A HREF="#_______">__________</A><BR>
|
||
|
||
- <A HREF="#_______">__________</A><BR>
|
||
|
||
- <A HREF="#_______">__________</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></IMG -->
|
||
</LI>
|
||
|
||
<!-- LI><A HREF="#_______">__________</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI -->
|
||
|
||
<!-- LI><A HREF="#_______">__________</A></LI -->
|
||
<!-- UL>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
|
||
<LI><A HREF="#ViewIndividualRecord"><B>View details for individual structure record</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#SummaryPage">Illustrated example</A></LI>
|
||
<LI><A HREF="#MmdbsrvSave">Save structure</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
</UL>
|
||
|
||
<!-- LI><A HREF="#_______"><B>__________</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI -->
|
||
|
||
</UL>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
|
||
</TD>
|
||
|
||
<!-- ========================== SPACER_CELL ================================= -->
|
||
|
||
<TD width="15"> </TD>
|
||
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ===== END_TABLE_WITH_MINI_TOC_AND_THUMBNAIL_SEARCH_RESULTS_DOCSUM ===== -->
|
||
|
||
<BR>
|
||
|
||
|
||
<!-- ========== BEGIN_LEVEL_1_DOCSUM_DISPLAY_MENU_DISPLAY_SETTINGS ============ -->
|
||
|
||
<A NAME="DisplaySettings"></A>
|
||
<A NAME="DocSumDisplaySettings"></A>
|
||
<A NAME="DocSumDisplayOptions"></A>
|
||
<A NAME="DocSumDisplayMenu"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Display settings</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
The "Display settings" menu on acts upon <B>all of the structure records</B> (default) in your <A HREF="#SearchResults">search results</A>, or on the <B>subset you have selected with checkboxes</B>. You can select items from multiple pages of the search results, if desired.<BR><BR>
|
||
|
||
|
||
<!-- =========== BEGIN_DOCSUM_DISPLAY_SETTINGS_TABLE =========== -->
|
||
|
||
<A NAME="SearchResultsDisplaySettings"></A>
|
||
<A NAME="DocSumDisplayMenuRecordFormats"></A>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="black 1px" cellpadding="4" class="format1 TableText1">
|
||
|
||
<!-- TR>
|
||
<TD class="format1H" width="20%" align="center" style="white-space: nowrap;"><b>Menu Name</b></TD>
|
||
<TD class="format1H" align="center"><b>Comments</b></TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="DocSumFormat"></A><B>Format</B></TD>
|
||
<TD class="format1B" valign="top">
|
||
<!-- A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A -->
|
||
|
||
<LI><A NAME="DocSumFormatSummary"></A><B>Summary</B> -- a summary of all of the structure records (default) retrieved by your search, or for those you have selected with checkboxes, in <B>HTML format</B>.<!-- By default, all records from your search result are listed. If you are interested only in specific records, select their checkboxes, select the desired display settings, and press "Apply" to view only those records. -->The information shown for each record may include the following, as available:
|
||
|
||
<UL>
|
||
<LI><A href="#MmdbsrvDescription">Title (description)</A> of the structure record</LI>
|
||
<LI><A href="#SearchFieldECRNnumber">Enzyme Commission (EC) number</A>, if available</LI>
|
||
<LI><A HREF="#MmdbsrvTaxonomy">Taxonomy (source organism(s))</A> of the protein and/or nucleotide sequences that comprise the structure </LI>
|
||
<LI><A HREF="#MmdbsrvMolecularComponents">Molecular components (proteins, nucleic acids, chemicals)</A> present the structure </LI>
|
||
<LI><A HREF="#SearchFieldMMDBModifyDate">Modification date</A></LI>
|
||
<LI><A HREF="#MmdbsrvMMDBID">MMDB ID</A> and <A href="#MmdbsrvPDBID">PDB ID</A></LI>
|
||
<LI>A subset of links to additional information about the structure, including a "<A HREF="../../icn3d/docs/icn3d_about.html"><B>View in iCn3D</B></A>" link that opens an interactive view of the 3D structure in NCBI's free web-based structure viewing program, as well as <A href="#DocSumLinks"><B>links to related data</B></A> in other Entrez databases. (Note: The "<B>Find Related Data</B>" menu in the right margin of the search results page provides a complete list of links. That menu retrieves related data for all records (default) retrieved by your search, or for the subset of records you have selected with checkboxes.)</LI>
|
||
</UL>
|
||
|
||
</LI>
|
||
|
||
<LI><A NAME="DocSumFormatSummaryText"></A><B>Summary (text)</B> -- a summary of the records retrieved by your search, in <B>plain text format</B>. By default, all records from your search result are listed. If you are interested only in specific records, select their checkboxes, select the desired display settings, and press "Apply" to view only those records. The information shown for each record is the same as in the "<A HREF="#DocSumFormatSummary">Summary</A>" format described above, but does not include the subset of links to additional information.</LI><BR><BR>
|
||
|
||
<LI><A NAME="DocSumFormatUIList"></A><B>UI List</B> -- a list of the <A HREF="#SearchFieldUID">unique identifiers (UI's)</A> for all of the structure records (default) retrieved by your search, or for those you have selected with checkboxes.</LI><BR><BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="DocSumShow"><B>Items per page</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<!-- A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A -->
|
||
<LI>By default, 20 documents are listed per page. If desired, decrease (to a minimum of 5) or increase (to a maximum of 200) the number of documents displayed per page then press the "Apply" button.</LI><BR><BR></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="DocSumSort"><B>Sort by</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<!-- A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A -->
|
||
<LI>Search results are displayed in order of decreasing relevance with respect to the query. Many <A HREF="#SearchFields">search fields</A> have a score or rank associated with them; for example, the <A HREF="#SearchFieldTitle">Title</A> and <A HREF="#SearchFieldOrganism">Organism</A> fields have a high rank, while the <A HREF="#SearchFieldPdbComment">PdbComment</A> field has a lower rank. The presence of a search term in any one or more of the fields is scored accordingly by the search system, and the total score given to a hit is used in determining its relevance to the query and therefore its placement on the search results page.</LI><BR><BR>
|
||
|
||
<LI>Additional options are available to sort records by descending or ascending order of <A HREF="#SearchFieldPdbAcc">PDB Accession</A>, <A HREF="#SearchFieldPDBDepositDate">PDB Deposit Date</A>, <A HREF="#SearchFieldMMDBEntryDate">MMDB Entry Date</A>, <A HREF="#SearchFieldProteinMoleculeCount">Protein Molecule Count</A>, <A HREF="#SearchFieldDNAMoleculeCount">DNA Molecule Count</A>, <A HREF="#SearchFieldRNAMoleculeCount">RNA Molecule Count</A>, and <A HREF="#SearchFieldChemicalCount">Chemical Count</A>.</LI><BR><BR>
|
||
|
||
<LI><I>Technical note</I>: If you retrieve all records in the database by searching the <A HREF="#SearchFieldFilter">Filter</A> field for <I>All[Filt]</I>, the records are simply displayed in descending order of <A HREF="#SearchFieldUID">UID</A> (i.e., MMDB ID).</LI><BR><BR>
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
<!-- ========== END_DOCSUM_DISPLAY_SETTINGS_TABLE =========== -->
|
||
|
||
<A NAME="DocSumDisplayMenuRecordFormatsFootnote"></A>
|
||
<!-- B>*</B> The variation in BioSystem record formats on the <A HREF="#SearchResults">DocSum</A> (search results) page is most evident for biosystems that have <A HREF="#BSSummaryDescription">descriptions</A>, such as the records retrieved by a search for <A HREF="/sites/entrez?cmd=search&db=structure&Term=human+TCA+cycle"><B>human TCA cycle</B></A>. If a search retrieves primarily biosystems for which descriptions are not available, the various BioSystem record formats might appear very similar to each other. In all cases, click on the BSID or title of a hit to view its <A HREF="#SummaryPage">BioSystem record</A>.
|
||
|
||
<B>*</B> The "_____" and "_____" objects are found only on the <A HREF="#____">____ page</A>. They are not present in the "<A HREF="#_____">_____</A>" display. -->
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============== END_LEVEL_1_DOCSUM_DISPLAY_MENU ================ -->
|
||
|
||
|
||
<!-- ========== BEGIN_LEVEL_1_DOCSUM_SENDTO_MENU ============ -->
|
||
|
||
<A NAME="DocSumSendTo"></A>
|
||
<A NAME="DocSumSendToMenu"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>"Send To" menu</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
The "Send To" menu options act upon all the hits retrieved by your search (default), or those you have selected by using their checkboxes.<BR><BR>
|
||
|
||
<!-- =========== BEGIN_TABLE_SEND_TO_MENU =========== -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="black 1px" cellpadding="4" class="format1 TableText1">
|
||
|
||
<!-- TR>
|
||
<TD class="format1H" width="20%" align="center" style="white-space: nowrap;"><b>Menu Name</b></TD>
|
||
<TD class="format1H" align="center"><b>Comments</b></TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="DocSumSendToFile"><B>File</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<!-- A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A -->
|
||
|
||
<LI>Saves all the hits retrieved by your search into a plain text file, in either "Summary (text)" or "UI List" <A HREF="#DocSumFormat"><!-- A HREF="#DocSumDisplayMenu" -->format</A>.<!-- For example, if a search retrieves 23 records and they are being displayed in Summary format on the <A HREF="#SearchResults">search results window</A>, the "Send to: File" option will save all 23 hits in that format into a file, regardless of how many of those hits are being shown per page. --></LI><BR><BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="DocSumSendToClipboard"><B>Clipboard</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<!-- A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A -->
|
||
|
||
<LI>Copies all the hits retrieved by your search (default), or those you have selected with check boxes, into a <!-- A HREF="/books/NBK3827/#pubmedhelp.Saving_citations_tem" --><B>Clipboard</B>, which <B>temporarily stores</B> up to 500 items (they will be lost after <B>8 hours</B> of inactivity).<!-- For example, if a search retrieves 23 records, the "Send to: Clipboard" option will send all 23 hits (or only those you have selected) into the Clipboard. --><BR><BR>
|
||
|
||
Click on the "Clipboard: XX items" link in the upper right corner of the page to view the items in any <A HREF="#DocSumFormat"><!-- A HREF="#DocSumDisplayMenu" -->format</A> for up to 8 hours after your last activity in the database.<BR><BR>
|
||
|
||
The Clipboard will not add an item that is currently in the Clipboard; it will not create duplicate entries. You can remove items from the Clipboard, if desired.<BR><BR>
|
||
|
||
Entrez uses <A HREF="/books/NBK3827/#pubmedhelp.Cookies">cookies</A> to add your selections to the Clipboard. For you to use this feature, your Web browser must be set to accept cookies.<BR><BR>
|
||
|
||
Items in the Clipboard are represented by the search number #0, which may be used in Boolean search statements. For example, to limit the items you have collected in the Clipboard to those from human, use the following search: #0 AND human[organism]. This does not affect or replace the Clipboard contents.<BR><BR>
|
||
|
||
The <!-- A HREF="/books/NBK3827/#pubmedhelp.Saving_citations_tem" -->Clipboard's "<B>Send to</B>" menu offers you the same "File" and "<B>Collections</B>" options as offered on the original search results page. The latter option saves all items (default), or the subset of items selected with check boxes, <B>indefinitely</B> in the <A HREF="/books/NBK53590/">My NCBI Collections</A> section of your <A HREF="/books/NBK3842/"><!-- A HREF="/books/NBK3827/#pubmedhelp.My_NCBI" -->My NCBI</A> account.</LI><BR><BR>
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="DocSumSendToClipboard"><B>Collections</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<!-- A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A -->
|
||
|
||
<LI>Saves all the hits retrieved by your search (default), or those you have selected by using their checkboxes, into the <A HREF="/books/NBK53590/">My NCBI Collections</A> section of your <A HREF="/books/NBK3842/"><!-- A HREF="/books/NBK3827/#pubmedhelp.My_NCBI" -->My NCBI</A> account.<!-- For example, if a search retrieves 23 records, the "Send to: Collections" option will save all 23 hits (or only those you have selected) into one of your existing collections or it will create a new collection, as you desire. -->
|
||
</LI><BR><BR>
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
<!-- =========== END_TABLE_SEND_TO_MENU =========== -->
|
||
|
||
<!-- BR>
|
||
|
||
<P class="indent30">Additional details about these options are provided in the <a HREF="/books/NBK3827/">PubMed help document</a> and <a HREF="/books/NBK3837/">Entrez help document</a>.</P -->
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- =========== END_LEVEL_1_DOCSUM_SHOW_SORT_SENDTO_MENUS ============ -->
|
||
|
||
<!-- ============ BEGIN_LEVEL_1_FILTERS ================ -->
|
||
|
||
<A NAME="Filters"></A>
|
||
<A NAME="FilterYourResults"></A>
|
||
<A NAME="SearchResultsFilters"></A>
|
||
<A NAME="SearchResultsSubsets"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Filter your results</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
|
||
<TD ALIGN="left" VALIGN="top">
|
||
|
||
<!-- IMAGE WITH CALLOUTS, aligned at left of page -->
|
||
<!-- A HREF="____________"><IMG src="images/________.png" height="100" width="300" border="0" align="right" alt="____________."></A -->
|
||
|
||
The "<B>Filter your results</B>" area in the upper right corner of a search results page allows you to see <B>all</B> the records (default) retrieved by your search, or <B>subsets</B> of your search results that reflect commonly requested categories of records, and shows the corresponding <B>number of records</B> in each case.<BR><BR>
|
||
|
||
<!-- The "<B>All</B>" folder tab at the top of a search results page shows the <B>total number of records retrieved by your search</B>, and that set of records displayed by default.<BR><BR -->
|
||
|
||
The "<B>NMR</B>" and "<B>X-ray</B>" folder tabs show the number of structures in your search results that were resolved by those <A HREF="#DataTypeExperimentalMethods">experimental methods</A> and enable you to view those <B>subsets of your search results</B>, if desired. The <A HREF="#SelectedRecords">Refine your results</A> box enables you to view other subsets from your search results.
|
||
|
||
</TD>
|
||
|
||
<!-- TD width="10" ALIGN="right" VALIGN="top"> </TD -->
|
||
|
||
<!-- TD width="300" class="WhiteCellBlueEdgeAll" ALIGN="right" VALIGN="top">
|
||
<A HREF="____________"><IMG src="images/________.png" height="100" width="300" border="0" align="right" alt="____________."></A></TD -->
|
||
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============== END_LEVEL_1_FILTERS ================ -->
|
||
|
||
<!-- ======= BEGIN_LEVEL_1_REFINE_YOUR_RESULTS_WAS_SELECTED_STRUCTURES ======= -->
|
||
|
||
<A NAME="SelectedRecords"></A>
|
||
<A NAME="SelectedStructures"></A>
|
||
<A NAME="SearchResultsRefineYourResults"></A>
|
||
<A NAME="RefineYourResults"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Refine your results</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD ALIGN="left" VALIGN="top">
|
||
<!-- NARROW IMAGE, NO CALLOUTS -->
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=p53+AND+tumor+AND+suppressor&dopt=DocSum"><IMG src="images/p53_tumor_suppressor_selected_structures_Entrez3.png" height="730" width="210" border="0" align="right" alt="Illustration of a Refine Your Results box on an Entrez Structure search results page. The items in the box allow you to view specific subsets of your search results that may be of interest. Click on the image to open the current, live search results for the p53 tumor suppressor search featured in this example."></A>
|
||
<!-- WIDER IMAGE, WITH CALLOUTS -->
|
||
<!-- A HREF="/sites/entrez?cmd=search&db=structure&term=p53+AND+tumor+AND+suppressor&dopt=DocSum"><IMG src="images/p53_tumor_suppressor_selected_structures_with_border.png" height="715" width="365" border="0" align="right" alt="Illustration of a Refine Your Results box on an Entrez Structure search results page. The items in the box allow you to view specific subsets of your search results that may be of interest. Click on the image to open the current, live search results for the p53 tumor suppressor search featured in this example."></A -->
|
||
|
||
<!-- By default, the Entrez Structure <A HREF="#SearchResults">search results</A> display lists all of the records retrieved by your search. -->The "<B>Refine Your Results</B>" box that appears in the upper right corner of a <A HREF="#SearchResults">search results page</A> displays some aggregate information that characterizes your search results and allows you to view <!-- ALT: provides single click access to --> the corresponding <B>subsets of the retrieved structure records</B>, for example:<!-- As an example, open the current results of a search for <A HREF="/sites/entrez?cmd=search&db=structure&term=p53+AND+tumor+AND+suppressor&dopt=DocSum">p53 tumor suppressor</A> (the illustration at the right features the results of that search as of June 2010). Refine Your Results include the following, as available: --><BR><BR>
|
||
|
||
<UL>
|
||
<LI><A NAME="SelectedRecordsProteinDomainFamilies"><B>Protein Domain Families</B></A> - subsets of 3D structures in your search results that contain protein molecules annotated with <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A>, inferring protein function:</LI><BR><BR>
|
||
|
||
<UL>
|
||
<LI><A NAME="SelectedRecordsProteinDomainSpecificHits"><B>Families</B></A> - 3D structures containing at least one protein molecule annotated with a <A HREF="../../cdd/cdd_help.shtml#SpecificHit">specific hit</A> to a <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domain</A>, suggesting a high confidence level for the inferred function of the protein. Subsets under this header list the <B>top five conserved domains</B> found as <A HREF="../../cdd/cdd_help.shtml#SpecificHit">specific hits</A> in the structures retrieved by your search. The <B>number in parentheses</B> represents the subset of structures from your search results that contain one or more protein molecules annotated with a specific hit to the listed domain; <B>clicking on the number</B> will retrieve that subset of structure records. The "<B>All XX Families</B>" link will open a list of all the conserved domain models (in the <A HREF="/sites/entrez?db=cdd">Conserved Domain Database</A>) that had at least one specific hit to a protein component of any structure found by your search.</LI><BR><BR>
|
||
|
||
<LI><A NAME="SelectedRecordsProteinDomainSuperfamilies"><B>Superfamilies</B></A> - 3D structures containing at least one protein molecule annotated with a <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_types">any type of hit</A> to a <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domain</A>, inferring that protein's function and therefore its membership in a <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamily</A>. Subsets under this header show the <B>top five conserved domain superfamilies</B> found in the structures retrieved by your search. The <B>number in parentheses</B> represents the subset of structures from your search results that contain one or more protein molecules annotated with the listed superfamily; <B>clicking on the number</B> will retrieve that subset of structure records. The "<B>All XX CDD Superfamilies</B>" link will open a list of all the superfamilies (in the <A HREF="/sites/entrez?db=cdd">Conserved Domain Database</A>) that were annotated on proteins components of the structures found by your search.</LI>
|
||
</UL><BR><BR>
|
||
|
||
<LI><A NAME="SelectedRecordsComplexes"><B>Complexes</B></A> - subsets of 3D structures in your search results that contain specific combinations of <A HREF="#MmdbsrvMolecularComponents">molecular components</A>:</LI><BR><BR>
|
||
<UL>
|
||
<LI><A NAME="SelectedRecordsComplexesProteinProtein"><B>Protein-Protein</B></A> - 3D structures that contain at least two protein molecules.</LI>
|
||
<LI><A NAME="SelectedRecordsComplexesProteinDNA"><B>Protein-DNA</B></A> - 3D structures that contain at least one protein molecule and one DNA molecule.</LI>
|
||
<LI><A NAME="SelectedRecordsComplexesProteinRNA"><B>Protein-RNA</B></A> - 3D structures that contain at least one protein molecule and one RNA molecule.</LI>
|
||
<LI><A NAME="SelectedRecordsComplexesProteinChemical"><B>Protein-Chemical</B></A> - 3D structures that contain at least one protein molecule and one chemical.</LI>
|
||
</UL><BR><BR>
|
||
|
||
<LI><A NAME="SelectedRecordsLiterature"><B>Literature</B></A> - subsets of 3D structures in your search results that contain links to published literature:</LI><BR><BR>
|
||
<UL>
|
||
<LI><A NAME="SelectedRecordsPubMed"><B>PubMed</B></A> - 3D structures that contain links to bibliographic information (article title, authors, abstract, journal name, etc.) in the <A HREF="/pubmed/">PubMed</A> database, for publications that describe the structures.</LI>
|
||
<LI><A NAME="SelectedRecordsPMC"><B>PMC</B></A> - 3D structures that contain links to full text articles that describe the structures in the <A HREF="/pmc/">PubMed Central (PMC)</A> free digital archive of biomedical and life sciences journal literature.</LI>
|
||
</UL><BR><BR>
|
||
|
||
<LI><A NAME="SelectedRecordsTaxonomy"><B>Taxonomy</B></A> - 3D structures that contain at least one <A HREF="#MmdbsrvMolecularComponents">molecular component</A> (protein or nucleotide sequence) from the various <A HREF="#SearchFieldOrganism">organisms</A> that were found in the search results.</LI><BR><BR>
|
||
<UL>
|
||
<LI>Subsets under this header show the five organisms most frequently found in the structures retrieved by your search. The <B>number in parentheses</B> represents the subset of structures from your search results that contain one or more protein molecules from the listed organism; <B>clicking on the number</B> will retrieve that subset of structure records. The "<B>All XX Organisms</B>" link shows the total number of different organisms found in the search results and opens that list of organisms in the <A HREF="/taxonomy/">NCBI Taxonomy</A> database.</LI>
|
||
</UL><!-- BR><BR -->
|
||
|
||
<!-- LI><A NAME="SelectedRecords_____"><B>______</B></A> - __________</LI>
|
||
<UL>
|
||
<LI><A NAME="SelectedRecords_____"><B>______</B></A> - __________</LI>
|
||
<LI><A NAME="SelectedRecords_____"><B>______</B></A> - __________</LI>
|
||
<LI><A NAME="SelectedRecords_____"><B>______</B></A> - __________</LI>
|
||
</UL><BR><BR -->
|
||
|
||
<!-- LI><A NAME="SelectedRecords_____"><B>______</B></A> - __________</LI -->
|
||
</UL>
|
||
|
||
</TD>
|
||
|
||
<!-- TD width="10" ALIGN="right" VALIGN="top"> </TD -->
|
||
|
||
<!-- TD width="355" class="WhiteCellBlueEdgeAll" ALIGN="right" VALIGN="top">
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=p53+AND+tumor+AND+suppressor&dopt=DocSum"><IMG src="images/p53_tumor_suppressor_selected_structures.png" height="705" width="355" border="0" align="left" alt="Illustration of a Refine Your Results box on an Entrez Structure search results page. The items in the box allow you to view specific subsets of your search results that may be of interest. Click on the image to open the current, live search results for the p53 tumor suppressor search featured in this example."></A></TD -->
|
||
|
||
<!-- TD width="365" class="WhiteCell" ALIGN="right" VALIGN="top">
|
||
<A HREF="/sites/entrez?cmd=search&db=structure&term=p53+AND+tumor+AND+suppressor&dopt=DocSum"><IMG src="images/p53_tumor_suppressor_selected_structures_with_border.png" height="715" width="365" border="0" align="left" alt="Illustration of a Refine Your Results box on an Entrez Structure search results page. The items in the box allow you to view specific subsets of your search results that may be of interest. Click on the image to open the current, live search results for the p53 tumor suppressor search featured in this example."></A></TD -->
|
||
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============== END_LEVEL_1_SELECTED_STRUCTURES ================ -->
|
||
|
||
|
||
|
||
<!-- ============== BEGIN_LEVEL_1_DOCSUM_LINKS_MENU ================ -->
|
||
|
||
<A NAME="DocSumLinks"></A>
|
||
<!-- BR -->
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Find related data</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD ALIGN="left" VALIGN="top">
|
||
<IMG src="images/1PTH_links_to_related_data_help_Entrez3.png" height="350" width="640" border="0" align="right" alt="Illustration of links to related data, which retrieve associated records from other Entrez databases, including as literature, protein and nucleotide sequences, bound chemicals, and more.">
|
||
As noted in the page on <A HREF="../../structure_discover.html">discovering associations among previously disparate data</A>, the <A HREF="/sites/gquery/"><B>Entrez</B></A> retrieval system is designed to provide integrated access to previously disparate data and make it possible to collect related information on a topic of interest within and across Entrez databases.<BR><BR>
|
||
|
||
As part of Entrez, the <A HREF="/sites/entrez?db=structure"><B>Structure database</B></A> implements a <A HREF="#DataProcessing">data processing</A> pipeline to identify such associations and present them as link options on <A HREF="#SearchResults">search results</A> pages.<BR><BR>
|
||
|
||
The <SPAN style="background-color: #FFFF00">"<B>Related information</B>"</SPAN> box that appears in the right margin of the display for an <B>individual record</B> allows you to retrieve related data for that particular structure. For example, if you select "<A HREF="#LinksDomains">Conserved Domains</A>" when you are viewing the record for accession <A HREF="/sites/entrez?cmd=search&db=cdd&term=cd00400[accn]&doptcmdl=summary" target="_new">1PTH</a>, you will retrieve the domain models from the Conserved Domain Database that have been annotated on the protein molecules in that structure. Many of the links are also available on a structure's <A HREF="#SummaryPage">summary page</A>.<BR><BR>
|
||
|
||
A <SPAN style="background-color: #FFFF00">"<B>Find Related Data</B>"</SPAN> box (instead of an "Related information" box) will appear in the right margin of an Entrez Structure <a href="#SearchResults"><B>search results</B></a> page if you retrieved <B>two or more records</B>. The "Find Related Data" box allows you to retrieve related data for <span style="color:#d70000">all</span> the records retrieved by your search (default), or for the records you have <span style="color:#d70000">selected</span> with checkboxes.<BR><BR>
|
||
|
||
The links in either display can include <A HREF="#LinksSimilarStructures"><B>Similar Structures</B></A>, <A HREF="#LinksLiterature"><B>Literature</B></A>, <A HREF="#LinksSequences"><B>Sequences</B></A>, <A HREF="#LinksDomains"><B>Domains</B></A>, <A HREF="#LinksChemicals"><B>Chemicals</B></A>, and <A HREF="#LinksOther"><B>Other Links</B></A>, depending on the related data that are available for the structures you have retrieved. (Note that the <A HREF="#LinksSimilarStructures">Similar Structures</A> link appears only on displays of individual records.)<BR><BR>
|
||
|
||
</TD>
|
||
|
||
<!-- TD width="10" ALIGN="right" VALIGN="top"> </TD>
|
||
|
||
<TD width="640" class="WhiteCellBlueEdgeAll" ALIGN="right" VALIGN="center">
|
||
<IMG src="images/1PTH_links_to_related_data_help.png" height="350" width="640" border="0" align="left" alt="Illustration of links to related data, which retrieve associated records from other Entrez databases, including as literature, protein and nucleotide sequences, bound chemicals, and more.">
|
||
</TD -->
|
||
|
||
</TR>
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- Some of the data accessible through these Links menus are also presented in <A HREF="#BSSummaryFolderTabs">folder tabs</A> on the individual BioSystem records.
|
||
Some of the folder tabs present the data in a different way (e.g., non-redundant view of sequence records in the <A HREF="#BSSummaryProteins">Proteins folder tab</A>) and/or provide additional functions (e.g., the ability to <A HREF="#BSSummaryHighightSelected">highlight selected components</A> in the source database's full size diagram). In addition, other small differences may exist, as noted in the descriptions of the <A HREF="#BSSummaryGenes">Genes</A> and <A HREF="#BSSummaryCitations">Citations</A> folder tabs.<BR><BR -->
|
||
|
||
<!-- ============= DOCSUM_LINKS_GROUP_RELATED_BIOSYSTEMS ============== -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="black 1px" cellpadding="4" class="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD class="format1H" align="left" style="white-space: nowrap;"><b>Link Group</b></TD>
|
||
<TD class="format1H" align="center" style="white-space: nowrap;"><b>Link Name</b></TD>
|
||
<TD class="format1H" align="center" style="white-space: nowrap;"><b>Description</b></TD>
|
||
</TR>
|
||
|
||
<!-- ============= DOCSUM_LINKS_GROUP_RELATED_STRUCTURES ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="LinksSimilarStructures"></A><A NAME="LinksSimilarStructures"><B>Similar Structures</B></A></TD>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><B>Similar Structures</B></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Other structures in MMDB that are similar in 3D shape to the selected structure, as determined by the original <A HREF="../../VAST/vast.shtml">VAST (<B>V</B>ector <B>A</B>lignment <B>S</B>earch <B>T</B>ool)</A>, and by <A HREF="../../vastplus/vastplus.cgi">VAST+</A>, during <A HREF="#DataProcessing">data processing</A>. (The similar structures are sometimes referred to as VAST or VAST+ "neighbors".)<!-- (The <A HREF="#DataProcessing">data processing</A>: <A HREF="#DataProcessingGeometricalFeatures">geometrical features</A> section provides more information about how the 3D domains and similar structures are identified.) --><BR><BR>
|
||
|
||
<A HREF="../../VAST/vast.shtml">VAST</A> identifies similar protein 3-dimensional structures by purely geometric criteria, in order to identify distant homologs that cannot be recognized by sequence comparison. The region of similarity can span the entire length of a protein molecule, or a portion of it. If a structure contains more than one protein molecule, similar structures are shown for each one.<BR><BR>
|
||
|
||
<A HREF="../../vastplus/vastplus.cgi">VAST+</A>, an expanded version of the program, has also been applied to each structure in MMDB in order to find macromolecular structures that have similarly shaped <A HREF="#DataProcessingBiologicalForms">biological units</A>, also referred to as "biounits".<BR><BR>
|
||
|
||
By <B>default</B>, VAST+ search results are shown for a structure, if/as available. If you prefer to see the original style VAST results, which focus on similarities between individual <!-- A HREF="#MmdbsrvMolecularComponents" --><A HREF="#MmdbsrvProteins">protein molecules</A> or <A HREF="#DataProcessing3dDomains">3D domains</A> (compact substructures)<!-- A HREF="../../cdd/cdd_help.shtml#CDWhat"><span style="color:#d70000">illustrated example</span></A -->) within the query structure and hits, follow the link for "<A HREF="../../vastplus/docs/vastplus_help.html#OriginalVAST"><B>original VAST</B></A>" near the upper right corner of the <A HREF="../../vastplus/vastplus.cgi">VAST+</A> search results page.<BR><BR>
|
||
|
||
The <A HREF="../../vastplus/docs/vastplus_help.html">VAST+ help document</A> provides details about the <A HREF="../../vastplus/docs/vastplus_help.html#Compare">differences between VAST and VAST+</A>, an <A HREF="../../vastplus/docs/vastplus_help.html#IllustratedExamples"><I><span style="color:#d70000">illustrated example</span></I> of VAST+ results</A>, and an <A HREF="../../vastplus/docs/vastplus_help.html#OriginalVASTDisplay"><I><span style="color:#d70000">illustrated example</span></I> of original VAST results</A>.<BR><BR>
|
||
|
||
<I>Additional notes:<BR><BR>
|
||
The "Similar Structures" link appears for individual records, as available. <B>Some structure records do not have any VAST neighbors</B> (<A HREF="../../vastplus/docs/vastplus_help.html#NullResult">read more</A>).<BR><BR>
|
||
|
||
The "Find related data:Structure" menu in the right margin of an <A HREF="#SearchResults">MMDB search results page</A> also enables you to retrieve similar structures. By default, that menu acts upon all of the items in your search results (i.e., it will retrieve the full set of structures that are are 3D-similar to any/all of the structures listed on your search results page). If you want to retrieve similar structures for only one record, or a subset of records from your search results, then activate the check boxes of the structures of interest before selecting "Find related data: Structure."<BR><BR>
|
||
|
||
"Similar Structures" are also accessible from the <A HREF="#SummaryPage">structure summary page</A>, either by clicking on the "<!-- A HREF="#LinksSimilarStructures" --><!-- A HREF="#LinksRelatedStructures" --><!-- A HREF="#MmdbsrvRelatedStructures" --><A HREF="#MmdbsrvSimilarStructures">Similar Structures: VAST+</A>" link near the upper right corner of the page, or by clicking on the colored bar that represents a protein molecule or 3D domain in the "<A HREF="#MmdbsrvProteinsFeatureAnnotations">show annotation</A>" graphic provided for each protein in the table of <A HREF="#MmdbsrvMolecularComponents">molecular components</A>.</I>
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ============= DOCSUM_LINKS_GROUP_LITERATURE ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="2"><A NAME="LinksLiterature"><B>Literature</B></A></TD>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksPMC"><B>PubMed Central Full Text</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Full text of cited references, if available in the <A HREF="/pmc/">PubMed Central</A> digital archive of biomedical and life sciences journal literature.</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksPubMed"><B>PubMed Citations</B></A></TD>
|
||
<TD class="format1B" valign="top"><A HREF="/pubmed/">PubMed</A> records for the reference(s) cited in the structure record.</TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksOMIM"><B>OMIM</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Records from the <A HREF="/sites/entrez?db=omim">Online Mendelian Inheritance in Man (OMIM)</A> database that are linked to the Entrez Gene records which in turn have been associated with a BioSystem during <A HREF="#DataProcessing">data processing</A>.</TD>
|
||
</TR -->
|
||
|
||
|
||
<!-- ============= DOCSUM_LINKS_GROUP_SEQUENCES ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="4"><A NAME="LinksSequences"><B>Sequences</B></A></TD>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksNucleotide"><B>Nucleotide</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Nucleotide sequences that comprise the 3D structure (see <A HREF="#MmdbsrvMolecularComponents">molecular components</A>). As noted in the <A HREF="#DataProcessing">data processing</A> section of this document, DNA or RNA sequence data present in 3D structure records are deposited into the <A HREF="/nuccore/">Entrez Nucleotide</A> database, and the "Nucleotide" link will retrieve those sequence records.
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksProtein"><B>Protein</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Protein sequence records that are directly associated with the structure record because at least one of the following is true:<BR><BR>
|
||
(a) the protein sequence record was <A HREF="#DataProcessingDeposition">created from</A> a 3D structure record (as described in the section on MMDB <A HREF="#DataProcessing">data processing</A><!-- A HREF="#DataProcessingDeposition">Deposit sequence and chemical data into Entrez Protein, Nucleotide, and PubChem databases</A -->)<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="50" height="1" border="0">or<BR>
|
||
(b) the accession number of the protein sequence record was listed in the "DBREF" record of the PDB source file. (The documentation about <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A> provides more information about the various "records" (data fields) that are present in PDB source files.)<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="50" height="1" border="0">or<BR>
|
||
(c) the protein accession found in the "DBREF" record of the PDB source file is also lists in an Entrez Gene record, and that Gene record also lists other protein accession(s); in such a case, the structure record will link to all of the protein accessions listed in the Entrez Gene record. (Those proteins will have reciprocal links back to the struture record, and will show a thumbnail image of a corresponding 3D structure in their protein sequence record display)<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="50" height="1" border="0">or<BR>
|
||
(d) the protein is identical in composition, sequence length, and source organism to any of the proteins noted in (b) or (c).
|
||
<!-- NOTE: Part (d) is true for all protein sequences EXCEPT patent records. Patent sequences and environmental sequences are numerous but infrequently used, so they are not included in PIGs, PIGpen. -->
|
||
<!-- WAS, through June 2012: Protein sequences that comprise the 3D structure (see <A HREF="#MmdbsrvMolecularComponents">molecular components</A>). As noted in the <A HREF="#DataProcessing">data processing</A> section of this document, protein sequence data present in 3D structure records are deposited into the <A HREF="/protein/">Entrez Protein</A> database, and the "Nucleotide" link will retrieve those sequence records. -->
|
||
</TD>
|
||
</TR>
|
||
|
||
<!--<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksProteinRelated"><B>Related Protein</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Proteins that are similar in sequence data to any one of the protein molecules in the 3D structure record. The similar proteins were identified using the <A HREF="../mmdb.shtml#CBLAST">CBLAST</A> program.</TD>
|
||
</TR>-->
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksGene"><B>Genes</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/gene/">Gene</A> records that correspond to the structure's protein components.<BR><BR>
|
||
The association between the structure record and a gene record is made in the following way:<BR><BR>
|
||
<UL>
|
||
<LI>When a 3D structure includes one or more protein molecules, it also includes sequence data for each protein molecule.</LI>
|
||
<LI>In addition to that sequence data, the structure record may also include a cross-reference other protein sequences (often Swiss-Prot) by listing their accession number in the "DBREF" record of the PDB source file. <I>(The documentation about <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A> provides more information about the various "records" (data fields) that are present in PDB source files.)</I></LI>
|
||
<LI>If the protein accession from the "DBREF" record is also listed in an Entrez Gene record, a link is created between the structure record and the Gene record.</LI>
|
||
</UL>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
|
||
<!-- ============= DOCSUM_LINKS_GROUP_DOMAINS ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="3"><A NAME="LinksDomains"><B>Domains</B></A></TD>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksConservedDomainFamily"><B>Conserved Domain Family</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="../../cdd/cdd_help.shtml#CDWhat">Conserved domains</A> that are <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hits</A> to the protein sequences that comprise the 3D structure (see <A HREF="#MmdbsrvMolecularComponents">molecular components</A>).</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksConservedDomainSuperfamily"><B>Conserved Domain Superfamily</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Conserved domain <A HREF="../../cdd/cdd_help.shtml#Superfamily">superfamilies</A> which include the domain models that were <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hits</A> to the protein sequences in the 3D structure.</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksConservedDomains"><B>Conserved Domains</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
The set of <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domain</A> models that get <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit">specific hits</A> or <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_non_specific_hit">non-specific hits</A> to the protein sequences in the 3D structure.</TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="Links3dDomains"><B>3D Domains</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Compact structural units within a protein that are identified automatically in MMDB using purely geometric criteria during <A HREF="#DataProcessing">data processing</A>. A protein molecule can contain one or more 3D domains, which often correspond with <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains (<span style="color:#d70000">illustrated example</span>)</A> observed in molecular evolution. Additionally, proteins that are dissimilar in sequence might contain geometrically similar 3D domains, indicating a distant homology that cannot be recognized by sequence comparison. 3D domains are used in the identification of <A HREF="#LinksSimilarStructures">VAST similar structures</A>.</TD>
|
||
</TR -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="Links___"><B>_______</B></A></TD>
|
||
<TD class="format1B" valign="top">____________.</TD>
|
||
</TR -->
|
||
|
||
|
||
|
||
<!-- ============= DOCSUM_LINKS_GROUP_CHEMICALS ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="2"><A NAME="LinksChemicals"><B>Chemicals</B></A></TD>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksPubChemCompound"><B>PubChem Compound</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=pccompound">PubChem Compound</A> records for bound chemicals present in the 3D structure record (see <A HREF="#MmdbsrvMolecularComponents">molecular components</A>). <!-- A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A>/<A HREF="#DataProcessingDirectLinksSmallMolecules"><B>small molecules</B></A> section of this document. --></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksPubChemSubstance"><B>PubChem Substance</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=pcsubstance">PubChem Substance</A> records for bound chemicals present in the 3D structure record (see <A HREF="#MmdbsrvMolecularComponents">molecular components</A>). <!-- A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A>/<A HREF="#DataProcessingDirectLinksSmallMolecules"><B>small molecules</B></A> section of this document. --></TD>
|
||
</TR>
|
||
|
||
<!-- ============= DOCSUM_LINKS_GROUP_SEQUENCES ============== -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="6"><A NAME="LinksSequences"><B>Sequences</B></A></TD>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksGenome"><B>Genome</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=genome">Entrez Genome</A> records that have been associated with a structure record using the method descibed in the <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A>/<A HREF="#DataProcessingDirectLinksGenomes"><B>genomes</B></A> section of this document.</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksNucleotide"><B>Nucleotide</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=nuccore">Entrez Nucleotide</A> records that have been associated with a structure using the method descibed in the <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A>/<A HREF="#DataProcessingDirectLinksNucleotides"><B>nucleotide</B></A> section of this document.</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksEST"><B>EST</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
____________.</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksGSS"><B>GSS</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
____________.</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksSNP"><B>SNP</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
____________.</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksProtein"><B>Protein</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=protein">Entrez Protein</A> records that have been associated with a biosystem using the method descibed in the <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A>/<A HREF="#DataProcessingDirectLinksProteins"><B>proteins</B></A> section of this document.</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DOCSUM_LINKS_GROUP_OTHER ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="4"><A NAME="LinksOther"><B>Other Links</B></A></TD>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksBioAssay"><B>BioAssay</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
If the protein in the structure record is the target of a bioassay, or involved in the biological process described in the bioassay experiment, a link between the structure record and the <A HREF="/sites/entrez?db=pcassay">PubChem BioAssay</A> record is established (if the submitter of the bioassay data provided the link to the structure record's protein).<!-- Yanli's suggested text, 07 Jan 2010: Here is the idea how the link is generated, please feel free to edit the English: "If the protein in the structure record is the target of a bioassay or involved in the biological process described in the bioassay experiment, a link between the structure record and the BioAssay record may be established". I used the word 'may' because it purely depends on whether the depositor provides this link, e.g. we are not doing the auto-link at this point by checking on the sequence and taxonomy identity between assay protein targets and proteins in MMDB (And if we do, we probably would probably end up with a few more PubChem BioAssay-MMDB links) -->
|
||
|
||
<!-- Original draft text: A structure record that includes a small molecule <A HREF="#MmdbsrvMolecularComponents">component</A> will have a <A HREF="#DataProcessingCreateLinks">direct link</A> to the <A HREF="/sites/entrez?db=pccompound">PubChem Compound</A> record for that small molecule, as noted above. If the PubChem Compound record in turn has a link to information about the molecule's biological activity in the <A HREF="/sites/entrez?db=pcassay">PubChem BioAssay</A> Database, a link between the structure record and the BioAssay record will also be established. --></TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksBioAssaysViaActives"><B>BioAssays via Actives</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=pccompound">PubChem Compound</A> records that have been associated with a biosystem (via the method descibed in the <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A>/<A HREF="#DataProcessingDirectLinksSmallMolecules"><B>small molecules</B></A>) might have links to the <A HREF="/sites/entrez?db=pcassay"><B>PubChem BioAssay</B></A> database. If they do, the <B>BioAssays via Actives</B> link retrieves the subset of bioassay records in which those compounds have been found to be active.<BR><BR>
|
||
<I>Note:  If you would like to see whether a specific compound (CID) has been found to be active in a bioassay record, click on the thumbnail image for the compound of interest at the bottom of the <A HREF="#SummaryPage"><B>structure summary page</B></A> to view the corresponding PubChem Compound record and see the various "Links" available for that record.</I></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksBioAssaysViaTarget"><B>BioAssays via Target</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Proteins that have been associated with a BioSystem (via the method descibed in <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A>/<A HREF="#DataProcessingDirectLinksProteins"><B>proteins</B></A>) might have their GI numbers cited as targets in <A HREF="/sites/entrez?db=pcassay"><B>PubChem BioAssay</B></A> records. If they do, the <B>BioAssays via Target</B> link retrieves the subset of bioassay records in which those proteins are targets of an assay.<BR><BR>
|
||
<I>Note:  If you would like to see whether a specific protein has been used as the target of a bioassay, open the corresponding protein sequence record and see the various "Links" available. If the protein's GI number is named as a target in a BioAssay record, the Links menu in the protein sequence record will include an option for "<B>BioAssay by Target</B>". If that GI was not specifically named as a target but an identical protein sequence (belonging to the same <A HREF="/ipg/">Identical Protein Group (IPG)</A>) [(belonging to the same protein identity group, or <A HREF="../../biosystems/docs/biosystems_help.html#PIG">PIG</A>)] was a target, the Links menu will include an option for "<B>BioAssay by Target, identical sequence</B>."</I></TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksBioSystem"></A><A NAME="LinksBioSystems"></A><B>BioSystem</B></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Biosystems that include protein sequences identical to any one of the protein molecules in a structure.
|
||
<BR><BR>
|
||
For example, if a <A HREF="../../biosystems/docs/biosystems_help.html#SummaryPage">biosystem record</A> lists a specific protein sequence record identification number (<A HREF="/Sitemap/samplerecord.html#GIpB">GI number</A>) as a biosystem component, the <A HREF="../../biosystems/docs/biosystems_help.html#DataProcessingDirectLinks">biosystem data processing procedure</A> will find all other sequences in the <A HREF="/protein/">Entrez Protein</A> database that are identical in composition and length. Such a group of identical proteins is called an "<A HREF="/ipg/">Identical Protein Group (IPG)</A>." <!-- (Such a group of identical proteins is called a "Protein identity group" or "PIG".) --> If one of those proteins is from a 3D structure record, a link will be established between that structure record and the biosystem.
|
||
<BR><BR>
|
||
<I>(The <A HREF="../../biosystems/docs/biosystems_help.html">BioSystems Database help document</A> <!-- also describes <A HREF="../../biosystems/docs/biosystems_help.html#LinksStructures">how links are created between structures and biosystems</A>, and provides brief information --> provides additional information about <A HREF="../../biosystems/docs/biosystems_help.html#IPG">identical protein groups</A>.)</I></TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksGenome"><B>Genome</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=genome">Entrez Genome</A> records that have been associated with a structure record {by what method?}</TD>
|
||
</TR -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksEST"><B>EST</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=nucest">Expressed Sequence Tags</A> (ESTs) that have been associated with a structure {by what method?}.</TD>
|
||
</TR -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksGSS"><B>GSS</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=nucgss">Genome Survey Sequences</A> (GSSs) that have been associated with a structure {by what method?}.</TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksOMIM"><B>OMIM</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
Records from the <A HREF="/sites/entrez?db=omim">Online Mendelian Inheritance in Man (OMIM)</A> database that cite one or more of the PubMed records associated with a structure<!-- (as described in <A HREF="#DataProcessing">data processing</A>) -->. For example, if an OMIM record cites a particular PubMed ID in its reference list, and that article is one of the cited references in a structure record, a link will be established from the structure to the OMIM record.</TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksSNP"><B>SNP</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
<A HREF="/sites/entrez?db=snp">Single Nucleotide Polymorphisms</A> (SNPs) and other small-scale insertions/deletions, polymorphic repetitive elements, and microsatellite variations that have been associated with a structure {by what method?}</TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="LinksTaxonomy"><B>Taxonomy</B></A></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
This link retrieves the <A HREF="/sites/entrez?db=taxonomy">NCBI Taxonomy</A> database record for the source organism(s) of the <A HREF="#MmdbsrvMolecularComponents">protein and/or nucleotide molecules</A> in the structure record. If a structure record contains protein or nucleotide sequences from more than one organism (e.g., <A HREF="/sites/entrez?cmd=search&db=structure&term=%22human%22%5BOrganism%5D+AND+HIV1%5BOrganism%5D&dopt=DocSum"><I>human and HIV1</I></A>), each source organism is listed and links to the corresponding taxonomic information in the <A HREF="/sites/entrez?db=taxonomy">NCBI Taxonomy</A> database, including the organism's Taxonomy ID (<A HREF="/books/NBK21100/#A268">TaxID</A>) and lineage.<!-- For additional information, see the <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A><A HREF="#DataProcessingDirectLinksTaxonomy"><B>taxonomy</B></A> section of this document. --></TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- B>*</B> The "_____" and "_____" objects are found only on the <A HREF="#____">____ page</A>. They are not present in the "<A HREF="#_____">_____</A>" display. -->
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============== END_LEVEL_1_DOCSUM_LINKS_MENU =================== -->
|
||
|
||
<!-- ============ LEVEL_1_VIEW_DETAILS_FOR_SINGLE_RECORD ============ -->
|
||
|
||
<A NAME="ViewIndividualRecord"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>View details for an individual structure record</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
Regardless of the <a href="#DocSumDisplayMenu">format</a> in which you have chosen to display your <A HREF="#SearchResults">search results</A>, simply click on the thumbnail image or title for a record of interest to view its <A HREF="#SummaryPage">structure summary page</A>.<BR><BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<BR>
|
||
|
||
|
||
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_5_CONTENTS ====== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_5_CONTENTS ############ -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ############### BLUE_HEADER_SECTION_6_SUMMARY_PAGE ############### -->
|
||
|
||
<A NAME="SummaryPage"></A>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Structure summary page:  What information is displayed for each structure?</SPAN></TD>
|
||
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############### END_BLUE_HEADER_SECTION_6_SUMMARY_PAGE ############### -->
|
||
|
||
|
||
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_6_CONTENTS ########### -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
||
<TR>
|
||
<TD class="WhiteCellBlueEdgeAll"><BR>
|
||
|
||
<!-- ====== TABLE_WITH_SAMPLE_STRUCTURE_RECORD_AND_MINI_TOC ======== -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD width="15"> </TD>
|
||
|
||
<!-- ======= IMAGE_SAMPLE_STRUCTURE_RECORD ======== -->
|
||
|
||
<TD width="650" ALIGN="LEFT" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
||
<TR>
|
||
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;">SAMPLE MMDB STRUCTURE SUMMARY PAGE for PDB ID 1PTH   <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885"><i>(open live page)</i></A><!-- br>
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885"><i>(open live MMDB summary page for 1PTH)</i></A --></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="WhiteCellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<TR>
|
||
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="WhiteCell">
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885"><IMG src="images/1PTH_structure_summary_biounits.png" width="635" height="975" border=0 align="center" alt="Annotated image of sample structure summary page, for sheep prostaglandin H2 synthase (MMDB ID 50885, PDB ID 1PTH). The READ MORE ABOUT column to the right of the image provides more details about each feature. Click on the image to open the live structure summary page in MMDB."></A>
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="Left" class="NormalText WhiteCell" VALIGN="TOP"> <BR> <BR></TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</TD>
|
||
|
||
<!-- ========================== SPACER_CELL ================================= -->
|
||
|
||
<TD width="10"> </TD>
|
||
|
||
|
||
<!-- ======= MINI_TABLE_OF_CONTENTS_FOR_STRUCTURE_RECORD ========== -->
|
||
|
||
<TD ALIGN="LEFT" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
||
<TR>
|
||
<TD ALIGN="CENTER" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;">READ MORE ABOUT:</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="WhiteCellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" class="WhiteCell">
|
||
|
||
<UL style="list-style-type: disc;padding:0px; margin:18px;">
|
||
|
||
<LI><A HREF="#MmdbsrvSearchButton"><B>Search box & button</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
|
||
<LI><A HREF="#MmdbsrvRecordIdentifiers"><B>Record Identifiers</B></A>
|
||
<BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR>
|
||
</LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvPDBID">PDB ID</A><!-- BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></IMG --></LI>
|
||
<LI><A HREF="#MmdbsrvMMDBID">MMDB ID</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
|
||
</UL>
|
||
|
||
<LI><A HREF="#MmdbsrvDescriptiveInfo"><B>Descriptive information</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvDescription">Title</A></LI>
|
||
<LI><A HREF="#MmdbsrvReference">Citation<!-- Reference --></A></LI>
|
||
<LI><A HREF="#MmdbsrvDeposited">PDB deposit date</A></LI>
|
||
<LI><A HREF="#MmdbsrvUpdatedInMMDB">MMDB update date</A><BR>
|
||
<!-- img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0"><A HREF="#MmdbsrvMMDBVersion">MMDB version</A></LI -->
|
||
<LI><A HREF="#MmdbsrvTaxonomy">Source organism</A></LI>
|
||
<LI><A HREF="#MmdbsrvSimilarStructures">Similar structures: VAST+</A></LI>
|
||
<!-- LI><A HREF="#MmdbsrvInferredInteractions">Inferred interactions: IBIS</A></LI -->
|
||
<LI><A HREF="#MmdbsrvExperimentalMethod">Experimental method</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
<!-- LI><A HREF="#MmdbsrvResolution">Resolution</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI -->
|
||
</UL>
|
||
|
||
<LI><A HREF="#MmdbsrvDisplayOptions"><B>Display Options</B></A>
|
||
<BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR>
|
||
</LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvDisplayOptionsConcise">Default Biological Unit</A></LI>
|
||
<LI><A HREF="#MmdbsrvDisplayOptionsComplete">All Biological Units</A><!-- BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></IMG --></LI>
|
||
<LI><A HREF="#MmdbsrvDisplayOptionsAsymmetric">Asymmetric Unit</A></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#MmdbsrvBiologicalUnit"><B>Biological Unit <I>N</I></B></A>
|
||
<BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR>
|
||
</LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvBiologicalUnit">Determined by...</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
</UL>
|
||
|
||
<LI><!-- A HREF="#MmdbsrvThumbnailImages" --><A HREF="#MmdbsrvStructureImages"><B>Structure Images</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#MmdbsrvThumbnailMolecularGraphic"><!-- 3D -->Molecular Graphic</A>
|
||
|
||
<!-- img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvThumbnailMolecularGraphicBiologicalForm">Biological Unit</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvThumbnailMolecularGraphicAsymmetricUnit">Asymmetric Unit</A><BR --><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0">
|
||
</LI>
|
||
|
||
<LI><A HREF="#MmdbsrvThumbnailSchematic">Interactions Schematic</A><BR>
|
||
|
||
<!-- img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvThumbnailSchematicMolecularComponents">Components</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvThumbnailSchematicInteractions">Interactions</A><BR -->
|
||
</LI>
|
||
|
||
</UL><BR>
|
||
|
||
<LI><A HREF="#MmdbsrvStructureView"><B>Download Structure Data</B></A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR></LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormat"><B>Format</B></A><BR>
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewFileFormatCn3D">ASN.1 (Cn3D)</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewFileFormatPDB">PDB</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewFileFormatXML">XML</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewFileFormatJSON">JSON</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewFileFormatPNG">PNG (image)</A><BR><BR>
|
||
|
||
<!-- img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewInJMol">JMol</A><BR -->
|
||
</LI>
|
||
|
||
|
||
<!-- LI><A HREF="#MmdbsrvStructureViewDisplayAs">Display As</A><BR>
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureView3DStructure">3D Structure</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewSeeFile">See File</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewSaveFile">Save File</A><BR -->
|
||
</LI>
|
||
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSet"><B>Data Set</B></A><BR>
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewDataSetAllAtoms">Single 3D Structure</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewDataSetAllModels">All 3D Structures</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewDataSetBackbone">Alpha Carbons</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvStructureViewDataSetPDBdataset">PDB source file</A><BR><BR>
|
||
</LI>
|
||
|
||
|
||
<LI><A HREF="#MmdbsrvSave"><B>Additional details</B></A><BR>
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0"><A HREF="#DownloadStructureDataIllustration">annotated illustration of download options</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0"><A HREF="#MmdbsrvSaveDataFile">scope of data saved</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0"><A HREF="#MmdbsrvSave3dView">save image</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0"><A HREF="#MmdbsrvSaveComponents">save structure components</A><BR><BR>
|
||
</LI>
|
||
|
||
</UL>
|
||
|
||
<LI><A HREF="#MmdbsrvMolecularComponents"><B>Molecular Components</B></A><!-- A HREF="#MmdbsrvAnnotations"><B>& Feature Annotations</B></A --><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvProteins"><B>Proteins</B></A><BR><!-- img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR -->
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0"><img SRC="../../IMG/spacer.gif" width="8" height="1" border="0"><A HREF="#MmdbsrvProteinsGeneSymbol">Gene symbol</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0"><img SRC="../../IMG/spacer.gif" width="8" height="1" border="0"><A HREF="#MmdbsrvProteins3dDomains">3D Domains</A><BR>
|
||
|
||
<img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0"><img SRC="../../IMG/spacer.gif" width="8" height="1" border="0"><A HREF="#MmdbsrvProteinsClassification">Domain Families (Protein classification)</A><BR>
|
||
|
||
<!-- img SRC="../../IMG/spacer.gif" width="5" height="1" border="0">
|
||
<img SRC="../../IMG/bullet_styles/A4_blue_triangle_8w_8h.png" width="8" height="8" border="0"></IMG --><img SRC="../../IMG/spacer.gif" width="5" height="5" border="0">
|
||
- <A HREF="#MmdbsrvProteinsClassificationSpecificHits">Specific Hits</A><BR>
|
||
|
||
<!-- img SRC="../../IMG/spacer.gif" width="5" height="1" border="0">
|
||
<img SRC="../../IMG/bullet_styles/A4_blue_triangle_8w_8h.png" width="8" height="8" border="0"></IMG --><img SRC="../../IMG/spacer.gif" width="5" height="5" border="0">
|
||
- <A HREF="#MmdbsrvProteinsClassificationSuperfamilies">Superfamilies</A><BR>
|
||
|
||
<!-- img SRC="../../IMG/spacer.gif" width="5" height="1" border="0">
|
||
<img SRC="../../IMG/bullet_styles/A4_blue_triangle_8w_8h.png" width="8" height="8" border="0"></IMG --><img SRC="../../IMG/spacer.gif" width="5" height="5" border="0">
|
||
- <A HREF="#MmdbsrvProteinsClassificationMultidomains">Multidomains</A>
|
||
|
||
|
||
<!-- img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0"> <A HREF="#MmdbsrvProteinsSimilarSequences">Similar Sequences (BLAST)</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"><BR -->
|
||
|
||
<!-- img SRC="../../IMG/bullet_styles/A3_blue_square_6w_6h.png" width="6" height="6" border="0">
|
||
<img SRC="../../IMG/spacer.gif" width="3" height="1" border="0">
|
||
<A HREF="#MmdbsrvProteinsSimilarStructures">Similar 3D Structures: VAST</A><BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0"></IMG -->
|
||
|
||
</LI>
|
||
|
||
<LI><A HREF="#MmdbsrvNucleotides"><B>Nucleotides</B></A><BR><!-- img SRC="../../IMG/spacer.gif" width="3" height="5" border="0" --></LI>
|
||
|
||
<LI><A HREF="#MmdbsrvChemicals"><B>Chemicals</B></A><!-- BR><img SRC="../../IMG/spacer.gif" width="3" height="5" border="0" --></LI>
|
||
|
||
<!-- LI><A HREF="#MmdbsrvInteractions">Observed [Inferred?] Interactions</A></LI -->
|
||
<!-- UL>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
|
||
|
||
<!-- LI><A HREF="#MmdbsrvStructureViewURLformat"><B>Web API</B>, URL format</A><BR>
|
||
|
||
<UL>
|
||
<LI><A HREF="#StructureViewURLformatBaseURL">Base URL</A></LI>
|
||
<LI><A HREF="#StructureViewURLformatParameters">Parameters</A></LI>
|
||
<LI><A HREF="#StructureViewURLformatExamples">Examples</A></LI>
|
||
</UL -->
|
||
|
||
</LI>
|
||
|
||
</UL>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
</TD>
|
||
|
||
<!-- ========================== SPACER_CELL ================================= -->
|
||
|
||
<TD width="15"> </TD>
|
||
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ======= END_TABLE_WITH_MINI_TOC_AND_THUMBNAIL_BIOSYSTEM_RECORD ========== -->
|
||
|
||
<A NAME="MmdbsrvSearchBox"></A>
|
||
<A NAME="MmdbsrvSearchButton"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3">Search box & button</SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
The "Search" box and button in the upper right hand corner of a <A HREF="#SummaryPage">structure summary page</A> allow you to retrieve a 3D structure record directly from the backend database by entering its unique identifier (UID), in the form of a <A HREF="#MmdbsrvPDBID">PDB accession</A> or an <A HREF="#MmdbsrvMMDBID">MMDB ID</A>. If you would like to search for structures using other methods, such as text term search, protein sequence query, or the 3D coordinates of a resolved structure, you can access those options from the MMDB <A HREF="mmdb_search.html">search methods</A> page.
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- =========== MMDBSRV_RECORD_IDENTIFIERS_MMDB_ID_AND_PDB_ID ============ -->
|
||
|
||
<A NAME="MmdbsrvRecordIdentifiers"></A>
|
||
<A NAME="MmdbsrvUID"></A>
|
||
<A NAME="UID"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3">Structure Record Identifiers</SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<A NAME="MmdbsrvPDBID"></A>
|
||
<A NAME="PDBID"></A>
|
||
<B>PDB ID</B>:  The accession of number of the <A HREF="http://www.rcsb.org/pdb/">Protein Data Bank (PDB)</A> record from which the MMDB record was derived. It is generally an alphanumeric combination (e.g., <A HREF="http://www.rcsb.org/pdb/explore/explore.do?pdbId=1PTH">1PTH</A>, which served as the source record for MMDB ID <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885">50885</A>). The PDB ID on the <A HREF="#SummaryPage">structure summary page</A> links to the source record on the PDB web site. <!-- I>(The PDB ID on a <A HREF="#SearchResults">search results page</A> opens that record in MMDB.)</I --> If <B>two or more PDB IDs</B> are listed on a structure summary page, that indicates the MMDB record has been <A HREF="#DataProcessingMergeSplitFiles">merged from PDB split files</A>. By merging the files, MMDB enables you to view and/or save the complete structure, as shown in the <A HREF="#DataProcessingMergeSplitFilesExampleRibosome">illustrated example</A> of the ribosome.<BR>
|
||
|
||
<BLOCKQUOTE>
|
||
<I>The <B>"Download" button</B> beside the PDB ID<!-- (in the upper right corner of a <A HREF="#SummaryPage">structure summary page</A>) --> downloads the original <A HREF="#SourceDatabases">PDB source file</A> from which the MMDB record was derived. That file contains data for the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> of the structure.<BR><BR>
|
||
Note that the "<A HREF="#MmdbsrvStructureView">Download Structure Data</A>" section of a structure summary page also provides a "PDB" option in the "Format" pulldown menu. That option does not save a copy of the PDB source file, but instead saves copy of the structure record, in <A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A>, after it has undergone <A HREF="#DataProcessing">MMDB data processing</A>.<BR><BR>
|
||
The differences are explained in a separate section of this document on "<A HREF="#MmdbsrvSave">additional details about structure data download options</A> > <A HREF="#MmdbsrvSavePDBformat">PDB format</A> > <A HREF="#MmdbsrvSavePDBformatDetails">details about the data that are saved</A>."</I>
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<A NAME="MmdbsrvMMDBID"></A>
|
||
<A NAME="MMDBID"></A>
|
||
<B>MMDB ID</B>:  The unique identifier of the structure record in the <A HREF="/sites/entrez?db=structure">Molecular Modeling Database (MMDB)</A>. It is a string of digits <!-- an integer --> (e.g., <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885">50885</A> for sheep prostaglandin H2 synthase) that are assigned consecutively to each structure record processed by NCBI. (This is also referred to as the structure's unique identifier, or <A HREF="#SearchFieldUID">UID</A>.)
|
||
|
||
<BLOCKQUOTE><I>Note: The MMDB data processing pipeline will assign a <B>new MMDB ID</B> number to a structure if the 3D coordinates and/or sequence data in the corresponding <A HREF="#SourceDatabases">PDB source file</A> have changed as a result of updates to the structure record. (The <A HREF="#PDBID">PDB ID</A> will remain the same, however.)<BR><BR>
|
||
|
||
For example, if the atoms in a previously available PDB data file were re-ordered during a PDB remediation the PDB accession will remain the same but it will receive a new <!-- A HREF="#SearchFieldUID" --><A HREF="#MmdbsrvMMDBID">MMDB ID</A> and a new <A HREF="#SearchFieldMMDBEntryDate ">MMDBEntryDate</A>.</I>
|
||
<!-- I>Previous versions of a structure record are still available through the "<B>MMDB Version</B>" menu, as explained below, under "<A HREF="#MmdbsrvDescriptiveInfo">Descriptive information</A> > <A HREF="#MmdbsrvUpdatedInMMDB">Updated in MMDB</A> > <A HREF="#MmdbsrvMMDBVersion">MMDB version</A>."</I -->
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- BLOCKQUOTE><I>Note: If the 3D coordinates and/or sequence data in a PDB source file change as a result of updates to the structure record, the MMDB data processing pipeline will assign a new MMDB ID number to that record, although the PDB ID remains the same. The previous versions of a structure record can also be viewed, as explained below, under <A HREF="#MmdbsrvDescriptiveInfo">Descriptive information</A> > <A HREF="#MmdbsrvUpdatedInMMDB">Updated in MMDB</A> > <A HREF="#MmdbsrvMMDBVersion">MMDB version</A>.</I>
|
||
</BLOCKQUOTE -->
|
||
|
||
<A NAME="MmdbsrvLinks"></A>
|
||
<!-- B>Links to related data</B>:  The pop-up menus that appear in the upper right corner of a structure record allow you to retrieve related biosystems, literature, biosystem components such as genes, sequences, and small molecules, and more. These pop-up menus also appear on <A HREF="#SearchResults">DocSum (search results) pages</A> and are explained in detail in that section of the help document, under <A HREF="#DocSumLinks"><B>links to related data</B></A>.<BR><BR -->
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
|
||
<!-- ============== MMDBSRV_DESCRIPTIVE_INFO ================ -->
|
||
|
||
<A NAME="MmdbsrvDescriptiveInfo"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Descriptive Information</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<A NAME="MmdbsrvTitle"></A>
|
||
<A NAME="MmdbsrvDescription"></A>
|
||
<B>Title</B>:  The title of the structure record, derived from the TITLE field of the PDB source file. It may or may not be the same as the title of the citation.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvReference"></A>
|
||
<B>Citation<!-- Reference --></B>:  The primary journal article that describes the structure. The article title opens the corresponding <A HREF="/pubmed/">PubMed</A> record. If additional references about the structure are available, an "All References" link will be present and will retrieve the primary as well as additional references from PubMed.<!-- (Note: Some structure records will display a "no primary citation" message, but will have a link for "additional references." This happens if the submitter of a structure record included a publication but did not flag it as the primary citation.) --> Reference information will be absent from summary pages of structures that do not have any corresponding publications.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvDeposited"></A>
|
||
<A NAME="MmdbsrvDeposition"></A>
|
||
<A NAME="MmdbsrvPDBDepositDate"></A>
|
||
<A NAME="MmdbsrvPDBDepositionDate"></A>
|
||
<B>PDB Deposition Date</B>:  The date on which the record was deposited into the Protein Data Bank. It is extracted from the HEADER record of the PDB source file and is searchable in the <A HREF="#SearchFieldPDBDepositDate">PDBDepositDate</A> field of MMDB. Note that this is not necessarily the date on which the record became publicly available, and may be significantly different from the release date if submitters requested their data remain confidential until publication.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvUpdatedInMMDB"></A>
|
||
<A NAME="MmdbsrvMMDBUpdateDate"></A>
|
||
<A NAME="MmdbsrvMMDBModifyDate"></A>
|
||
<B>Updated in MMDB</B>:  The date on which the record was last modified. This may reflect the date on which a new version of the PDB source record was imported into MMDB, or the date on which changes were made to MMDB's version of the record as a result of enhancements to NCBI <A HREF="#DataProcessing">data processing</A> procedures, and is searchable in the <A HREF="#SearchFieldMMDBModifyDate">MMDBModifyDate</A> field of MMDB.
|
||
|
||
<BLOCKQUOTE>
|
||
<I>Note: You can use the <A HREF="#SearchFieldMMDBModifyDate">MMDBModifyDate</A> search field of MMDB to retrieve records that were modified on a given date or between a <A HREF="#SearchMethodRangeQuery">range</A> of dates.<BR>
|
||
If no modifications were made since the record was deposited into MMDB, then MMDBModifyDate will be the same as the <A HREF="#SearchFieldMMDBEntryDate">MMDBEntryDate</A>.<BR>
|
||
If PDB undergoes a database remediation, in which most or all PDB records are updated in some way, many or all records will share the same update date. (<A HREF="#SearchFieldMMDBModifyDate">more...</A>)<BR>
|
||
If the 3D coordinates and/or sequence data in a PDB source file change as a result of updates to the structure record, the MMDB data processing pipeline will assign a new <A HREF="#MmdbsrvMMDBID">MMDB ID</A> number to that record, although the PDB ID remains the same.</I>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- BLOCKQUOTE><A NAME="MmdbsrvMMDBVersion"></A><A NAME="MMDBVersion"></A><B>MMDB Version</B>:  [Click on the down arrow to the right of the "Updated in MMDB" date to open an "MMDB Version" menu, which allows you to select/view previous versions of the structure record.] The most recent version of a structure record is displayed by default. However, you can also to view/save earlier versions of the record by clicking on the down arrow to the right of the "<A HREF="#MmdbsrvUpdatedInMMDB">Updated in MMDB</A>" date. That will open an <I>"MMDB Version" menu</I>.<BR><BR>
|
||
|
||
The versions reflect changes that have been made to the PDB source file (e.g., content revisions made by the author, or file format/content changes that occurred as a result of PDB data processing and/or PDB remediations), or changes that have been made to MMDB's version of the structure record as a result of enhancements to the <A HREF="mmdb_help.html#DataProcessing"> MMDB data processing</A> procedures. The changes that occur from one version to another can vary from minor text changes in descriptive information (e.g., references, comments, etc.) to changes in the 3D coordinate and/or sequence data.<BR><BR>
|
||
|
||
If the structure record's [<A HREF="#SearchFieldUID">]<A HREF="#MmdbsrvMMDBID">MMDB ID</A> has changed from one version to another, that indicates the <A HREF="#SourceDatabases">PDB source file</A> contained [{{significant}}] changes in the 3D coordinate and/or sequence data compared to the earlier version. For example, if the atoms in a previously available PDB data file were re-ordered during a PDB remediation (e.g., <A HREF="http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2007.html#20070904">September 2007</A> or <A HREF="http://www.pdb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20090317a">March 2009</A> remediations), the PDB accession will remain the same but it will receive a new [<A HREF="#SearchFieldUID">]<A HREF="#MmdbsrvMMDBID">MMDB ID</A> and a new <A HREF="#SearchFieldMMDBEntryDate ">MMDBEntryDate</A>.<BR><BR>
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||
|
||
</BLOCKQUOTE -->
|
||
|
||
<A NAME="MmdbsrvTaxonomy"></A>
|
||
<A NAME="SourceOrganism"></A>
|
||
<B>Source Organism</B>:  The source organism(s) of the <A HREF="#MmdbsrvMolecularComponents">protein and/or nucleotide molecules</A> in the structure record. If a structure record contains protein or nucleotide sequences from more than one organism (e.g., <A HREF="/sites/entrez?cmd=search&db=structure&term=%22human%22%5BOrganism%5D+AND+HIV1%5BOrganism%5D&dopt=DocSum"><I>human AND HIV1</I></A>), each source organism is listed and links to the corresponding taxonomic information in the <A HREF="/sites/entrez?db=taxonomy">NCBI Taxonomy</A> database, including the organism's Taxonomy ID (<A HREF="/books/NBK21100/#A268">TaxID</A>) and lineage.<!-- For additional information, see the <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A><A HREF="#DataProcessingDirectLinksTaxonomy"><B>taxonomy</B></A> section of this document. --><BR><BR>
|
||
|
||
<A NAME="Resolution"></A>
|
||
<A NAME="MmdbsrvResolution"></A>
|
||
<B>Resolution</B>:  The resolution of the structure in Angstroms (Å), extracted from the REMARK 2 record of the PDB source file.<!-- Å is the HTML code for Angstrom, <20> --> The PDB website provides <A HREF="http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/resolution.html">additional information</A> about resolution.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvExperimentalMethod"></A>
|
||
<B>Experimental Method</B>:  The <A HREF="#DataTypeExperimentalMethods"> experimental method </A> that was used to resolve the structure, extracted from the "EXPDTA" record of the PDB source file.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvSimilarStructures"></A>
|
||
<A NAME="MmdbsrvRelatedStructures"></A>
|
||
<A NAME="MmdbsrvRelatedStructure"></A>
|
||
<A NAME="VAST"></A>
|
||
<B>Similar Structures: VAST+</B>:  The "Similar Structures: VAST+" link near the upper right hand corner of a <A HREF="#SummaryPage">structure summary page</A> allows you to retrieve the <SPAN style="background-color: #FFFF00"><B>structures that are similar in 3D shape</B></SPAN> to the one currently being viewed.
|
||
|
||
<BLOCKQUOTE>
|
||
The similar structures were found by the <SPAN style="background-color: #FFFF00"><A HREF="../../VAST/vast.shtml"><B>V</B>ector <B>A</B>lignment <B>S</B>earch <B>T</B>ool (<B>VAST</B>)</A></SPAN>, which identifies structures that are similar in 3D shape, using purely geometric criteria, regardless of their degree of sequence similarity. In this way, VAST can identify distant homologs that cannot be recognized by sequence comparison.<BR><BR>
|
||
|
||
The default "Similar Structures" display shows the <SPAN style="background-color: #FFFF00"><A HREF="../../vastplus/vastplus.cgi"><B>VAST+</B></A></SPAN> search results page, which lists the query structure followed by similar structures, ranked by their degree of similarity to the query structure's <B>macromolecular complex</B> (<SPAN style="background-color: #FFFF00"><A HREF="#DataProcessingBiologicalForms"><B>biological unit</B></A></SPAN>). It firsts lists <A HREF="../../vastplus/docs/vastplus_help.html#OutputFilterCompleteMatch"><IMG SRC="../../vastplus/docs/images/icon_red_circle_solid.png" WIDTH="10" HEIGHT="10" BORDER="0" ALT="Solid red circle icon that appears beside similar structures that have a complete match to the biological unit of the query protein structure."> complete matches</A> to the query structure's biological unit, followed by <A HREF="../../vastplus/docs/vastplus_help.html#OutputFilterPartialMatch"><IMG SRC="../../vastplus/docs/images/icon_red_circle_half_filled.png" WIDTH="10" HEIGHT="10" BORDER="0" ALT="Half filled red circle icon that appears beside similar structures that have a partial match to the biological unit of the query protein structure.">partial matches</A>, and ending with matches to individual protein molecules. (<A HREF="../../vastplus/docs/vastplus_help.html#IllustratedExamples"><I><span style="color:#d70000">Illustrated examples of VAST+ results</span>.</I></A>)<BR><BR>
|
||
|
||
If you prefer to see the <SPAN style="background-color: #FFFF00"><B>Original</B> <A HREF="../../VAST/vast.shtml"><B>VAST</B></A></SPAN> results, which focus on similarities between <B>individual</B> <!-- A HREF="#MmdbsrvMolecularComponents" --><A HREF="#MmdbsrvProteins"><B>protein molecules</B></A>, or <B>individual</B> <A HREF="#DataProcessing3dDomains"><B>3D domains</B></A> (compact substructures)<!-- A HREF="../../cdd/cdd_help.shtml#CDWhat"><span style="color:#d70000">illustrated example</span></A --> rather than macromolecular complexes, follow the link for "<A HREF="../../vastplus/docs/vastplus_help.html#OriginalVAST"><B>original VAST</B></A>" near the upper right corner of the <A HREF="../../vastplus/vastplus.cgi">VAST+</A> search results page. The Original VAST display page <B>lists</B> each <!-- A HREF="#MmdbsrvMolecularComponents"><A HREF="#MmdbsrvProteins" -->protein molecule and <A HREF="#DataProcessing3dDomains">3D domain</A> in the <SPAN style="background-color: #FFFF00"><A HREF="#AsymmetricUnit"><B>asymmetric unit</B></A></SPAN> of the query structure, and <B>links</B> to structures that are similar in shape to the protein molecule or 3D domain you select. <I>(<A HREF="../../vastplus/docs/vastplus_help.html#OriginalVASTDisplay"><span style="color:#d70000">Illustrated example of original VAST results</span>.</A>)</I><BR><BR>
|
||
|
||
Alternatively, Original VAST similar structures can be retrieved from the <A HREF="#SummaryPage">structure summary page</A> by scrolling down to the table of <A HREF="#MmdbsrvMolecularComponents">molecules and interactions</A>, viewing the the "<A HREF="#MmdbsrvProteinsFeatureAnnotations">show annotation</A>" graphic for a protein of interest, and then clicking on the bar graphic for the overall protein molecule or for any 3D domain it contains in order to view a list of structures that are similar in shape to the molecule or 3D domain you selected.<BR><BR>
|
||
|
||
The <A HREF="#DataProcessing">data processing</A>: <A HREF="#DataProcessingGeometricalFeatures">geometrical features</A> section of this document provides more information about how similar structures are identified. The <A HREF="../../vastplus/docs/vastplus_help.html">VAST+ help document</A> provides details about the <SPAN style="background-color: #FFFF00"><A HREF="../../vastplus/docs/vastplus_help.html#Compare"><B>differences between VAST and VAST+</B></A></SPAN><!-- A HREF="../../vastplus/docs/vastplus_help.html#IllustratedExamples"><I><span style="color:#d70000">illustrated examples</span></I> of VAST+ results</A>, and an <A HREF="../../vastplus/docs/vastplus_help.html#OriginalVASTDisplay"><I><span style="color:#d70000">illustrated example</span></I> of original VAST results</A -->. Additional details about VAST and VAST+ are provided in the articles listed on the <A HREF="../../VAST/docs/vast_publications.html">VAST publications</A> page<!-- and in the <A HREF="../../VAST/vasthelp.html">VAST help document</A> and <A HREF="../../vastplus/docs/vastplus_help.html">VAST+ help document</A -->.<BR><BR>
|
||
|
||
<I>(Note: if you have a new structure that is not yet publicly available in MMDB, you can use the <A HREF="../../VAST/vastsearch.html">VAST Search</A> page to input the coordinates of that newly resolved structure in <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A>, and compare it against all structures in MMDB to find its neighbors.)</I><BR><BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ========== IMAGE OF ORIGINAL VAST SIMILAR STRUCTURES TABLE ========== -->
|
||
|
||
<!-- P class="indent40"><A HREF="data/vast_alignment_of_1PTH_A_and_1EGQ_A.cn3"><IMG SRC="images/1PTH_structure_summary_vast_related_structures_individual_chains.png" WIDTH="800" HEIGHT="800" BORDER="1" ALT="Illustration of the compact substructures, called 3D domains, in the structure for 1PTH, sheep prostaglandin H2 synthase, and the list of Similar Structures that have a similar shape to the whole protein molecule or to any 3D domain within it. Click anywhere on this image to open an interactive view of the 3D alignment of protein A, domain 1, in 1PTH and a sample similar structure, 1EGQ. Install Cn3D before clicking, if that program is not yet on your computer."></A></P><BR -->
|
||
|
||
<!-- ========= END IMAGE OF ORIGINAL VAST SIMILAR STRUCTURES TABLE ========= -->
|
||
|
||
<!-- BLOCKQUOTE>
|
||
|
||
<A NAME="MmdbsrvInferredInteractions"></A>
|
||
<B>Inferred Interactions</B>:  The "<B>IBIS</B>" link will open the <A HREF="../../ibis/ibis.cgi"><B>I</B>nferred <B>B</B>iomolecular <B>I</B>nteractions <B>S</B>erver</A>, which reports physical interactions observed in experimentally-determined structures for each protein that was in your original query structure. IBIS also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation.<BR>
|
||
|
||
</BLOCKQUOTE -->
|
||
|
||
<!-- ======== MMDBSRV_DISPLAY_OPTIONS_CONCISE_COMPLETE_ASYMMETRIC ======== -->
|
||
|
||
<A NAME="MmdbsrvDisplayOptions"></A>
|
||
<A NAME="DisplayOptions"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3">Display Options</SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
The MMDB <A HREF="#DataProcessing">data processing pipeline</A> applies several <A HREF="#DataProcessingBiologicalFormsProcedures">procedures to identify</A> the <B>biochemically active forms of a biomolecule</B> ("<A HREF="#DataProcessingBiologicalForms"><B>biological units</B></A>") present within a structure record that has been resolved by x-ray crystallography or neutron diffraction of a crystal. The display options on an <A HREF="#SummaryPage">MMDB summary page</A> provide several views of the data in such records:<BR><BR>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<A NAME="MmdbsrvDisplayOptionsConcise"></A>
|
||
<A NAME="MmdbsrvDisplayOptionsDefaultBiounit"></A>
|
||
<A NAME="DefaultBiounit"></A>
|
||
<A NAME="DefaultBiologicalUnit"></A>
|
||
<B>Default Biological Unit</B>:  This option is selected by default and displays the first author-determined <A HREF="#DataProcessingBiologicalForms">biological unit</A> that is listed in the <A HREF="#SourceDatabases">PDB source file</A>. If a PDB source file lists only software-determined biounits, then the first one listed is displayed as the default biounit. Additional information about the <A HREF="#DataProcessingBiologicalFormsProcedures">identification of biological units</A> is provided in the <A HREF="#DataProcessing">data processing</A> section of this document.<!-- To find out if the default biological unit is author-determined or software-determined, view the PDB source file in PDB format and look at the remark 350 record, which will indicate the method by which each biological unit was determined. --></LI><BR><BR>
|
||
<!-- B>Unique Biological Units</B>:  This option is selected by default and displays only the <A HREF="#DataProcessingBiologicalFormsTypeClassification">distinct</A> biological units that were found in the structure record. If the structure record contains two or more biological units that were found to be similar to each other, only one of them is shown as a representative.</LI><BR><BR -->
|
||
|
||
<A NAME="MmdbsrvDisplayOptionsComplete"></A>
|
||
<A NAME="MmdbsrvDisplayOptionsAllBiounits"></A>
|
||
<A NAME="AllBiounits"></A>
|
||
<A NAME="AllBiologicalUnits"></A>
|
||
<B>All Biological Units</B>:  If two or more biological units were found in the structure record, this option will display <B>all biological units</B> that were found in the structure record, whether they are <A HREF="#DataProcessingBiologicalFormsTypeClassification">similar or distinct</A>, and whether they were <A HREF="#DataProcessingBiologicalFormsRemark350">author-determined or software-determined</A>. <!-- If the number of all biological units is greater than the number of unique biological units, this indicates the structure record contains two or more biological units that were found to be <A HREF="#DataProcessingBiologicalFormsTypeClassification">similar</A> to each other. --></LI><BR><BR>
|
||
|
||
<A NAME="MmdbsrvDisplayOptionsAsymmetric"></A>
|
||
<B>Asymmetric Unit</B>:  This option displays the data that were provided by the submitter of the record. These data are often casually referred to as the <A HREF="#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A> and can represent either: (a) the complete biological unit; (b) a portion of the biological unit; or (c) multiple copies of the biological unit, as shown in the illustrated example of three different <A HREF="#DataProcessingHumanHemoglobinExamples">human hemoglobin</A> structure records.
|
||
<!-- (a) the complete biological unit, (b) a portion of the biological unit, or (c) multiple copies of the biological unit (see illustrated example of <A HREF="#DataProcessingHumanHemoglobinExamples">human hemoglobin structures</A>). --> (Note: "Asymmetric unit" is the only display option for <A HREF="#DataProcessingMergeSplitFiles">merged PDB split files</A> from crystallographic studies.)
|
||
</LI><BR><BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
When you use the <B>options to</B> "<A HREF="#MmdbsrvStructureView"><B>Download Structure Data</B></A>," they <B>will act upon the biological unit(s) or asymmetric unit currently displayed</B> in the browser window. For example, if you are viewing the <A HREF="#DefaultBiologicalUnit">default biological unit</A> and choose to display the 3D structure, only that biological unit will be shown in the 3D structure viewer, regardless of how many copies of the biological unit exist in the raw data that were deposited by the submitter. To see the raw data, change the display to "asymmetric unit" before selecting the desired "View or Save 3D Structure" options.<BR><BR>
|
||
|
||
|
||
<I>Note:</I> <!-- As of May 2011, -->The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records resolved by x-ray crystallography or neutron diffraction of crystals. In such cases, all three of the above displays will be the same (i.e., default biological unit = all biological units = asymmetric unit). In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>, or it represents multiple copies of the biological unit. In those cases, the biological unit displays will be different from the asymmetric unit display.</I><BR><BR>
|
||
|
||
If you are viewing a structure resolved by an <A HREF="#DataTypeExperimentalMethods">experimental method</A> other than x-ray crystallography or neutron diffraction of a crystal, the above display options will <I>not</I> be present, as the concepts of asymmetric unit and biological unit do not apply to structures resolved by other methods.<BR><BR>
|
||
|
||
Finally, the "<!-- A HREF="#DataProcessingBiologicalForms" -->biological unit" display option is not available for <A HREF="#DataProcessingMergeSplitFiles">merged PDB split files</A> from <I>crystallographic</I> studies, because the biological unit of the complete structure is not specified in a computer readable way in the PDB source files. The <A HREF="#SummaryPage">structure summary</A> page for a merged crystallographic structure therefore simply uses the label of "asymmetric unit" above the molecular graphic, as it represents the unification of raw data from the original PDB files. The asymmetric unit can represent the structure's complete biological unit, a portion of the biological unit, or multiple copies of the biological unit. In the case of structures resolved by <I>electron microscopy (EM)</I> or <I>nuclear magnetic resonance (NMR)</I>, the term "asymmetric unit" does not apply, and the term "biological unit" is shown instead on the summary page for a merged structure from either of those technologies. Please refer to the corresponding publication for a structure, if/as available, for the author's description of its biologically active form. In such cases, please refer to the corresponding publication, if/as available, for the author's description of the structure's biologically active form.
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
|
||
<!-- ========= MMDBSRV_BIOLOGICAL_UNIT_N =========== -->
|
||
<A NAME="MmdbsrvBiologicalUnit"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Biological Unit <I>N</I></B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
For each <A HREF="#DataProcessingBiologicalForms">biological unit</A> <A HREF="#MmdbsrvDisplayOptions">displayed</A>, the <!-- A HREF="#SummaryPage" -->MMDB summary page:
|
||
|
||
<OL>
|
||
<LI>provides a <B>type</B> classification based on a <A HREF="#DataProcessingBiologicalFormsTypeClassification">comparison of the biological units</A> identified in the structure record, if the record contains multiple biological units. If two or more biological units meet a threshold for sequence and structural similarity, they will receive the same type code; if they do not meet that threshold, they are considered distinct from each other and received different type codes.</LI>
|
||
<LI>indicates the <B>oligomeric state</B> (dimer, trimer, tetramer, etc.) and the <A HREF="#DataProcessingBiologicalFormsProcedures">method</A> by which it was determined</LI>
|
||
<LI>presents a schematic diagram of <A HREF="#MmdbsrvThumbnailSchematic"><B>interactions</B></A>, a <A HREF="#MmdbsrvThumbnailMolecularGraphic"><B>molecular graphic</B></A>, <A HREF="#MmdbsrvStructureView">options to <B>download the structure data</B></A>, and a table of <A HREF="#MmdbsrvMolecularComponents"><B>molecular components</B></A>.</LI>
|
||
</OL>
|
||
|
||
If the asymmetric unit is <A HREF="#MmdbsrvDisplayOptions">displayed</A>, only a molecular graphic and table of molecular components will be shown (no interaction schematic).<BR><BR>
|
||
|
||
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
|
||
<!-- ========= MMDBSRV_STRUCTURE_IMAGES =========== -->
|
||
<!-- ========= WAS:MMDBSRV_THUMBNAIL_IMAGES =========== -->
|
||
|
||
<A NAME="MmdbsrvStructureImage"></A>
|
||
<A NAME="MmdbsrvStructureImages"></A>
|
||
<A NAME="MmdbsrvThumbnailImage"></A>
|
||
<A NAME="MmdbsrvThumbnailImages"></A>
|
||
<A NAME="MmdbsrvThumbnailImageDisplayOptions"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Structure Images</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<!-- ============== STRUCTURE_IMAGES ============= -->
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<!-- TR>
|
||
<TD valign="top" width="200"><A NAME="MmdbsrvThumbnailImageMain"><B>Thumbnail image</B></A> <A HREF="#ThumbnailImageConservedDomainRecord"><B>*</B></A></TD>
|
||
<TD valign="top" align="left">The main thumbnail image <A HREF="#ThumbnailImageConservedDomainRecord"><B>*</B></A> in the upper left corner of a <A HREF="#SummaryPage">structure summary page</A> shows a single, static snapshot of the 3D structure, generated by the <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> program. <B>Click</B> on the graphic to open an interactive view of the structure in Cn3D. Download that free program (available for PC, Mac, or Unix) before pressing the button, if it is not yet on your computer. [The free <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> program (available for PC, Mac, or Unix) must be present on your computer in order for this to work.]</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD colspan="3" valign="top">By default, the <A HREF="#SummaryPage">MMDB summary page</A> <A HREF="#MmdbsrvDisplayOptions">displays</A> a concise list of the <A HREF="#DataProcessingBiologicalForms">biological unit(s)</A> that were identified in the structure, showing both a <A HREF="#MmdbsrvThumbnailMolecularGraphic"><B>molecular graphic</B></A> and an <A HREF="#MmdbsrvThumbnailInteractionsSchematic"><B>interactions schematic</B></A> for each <A HREF="#DataProcessingBiologicalFormsTypeClassification">distinct biological unit</A>. If you choose to view the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>, the page will display only a molecular graphic (no interaction schematic) along with a note indicating the relationship between the asymmetric unit and the biological unit(s).</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="3" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="200"><A NAME="MmdbsrvMolecularGraphic"></A><A NAME="MmdbsrvThumbnailMolecularGraphic"></A><A NAME="MolecularGraphic"></A><B>Molecular Graphic</B><!-- was: A NAME="MmdbsrvThumbnailImageMain"><B>Thumbnail image</B></A --><BR><BR><IMG SRC="images/1PTH_thumbnail_molecular_graphic_from_mmdbsrv_page.png" WIDTH="150" HEIGHT="750" BORDER="0" ALT="Sample thumbnail molecular graphic for 1PTH, prostaglandin H2 synthase-1 from sheep. A static image is shown by default. Click the 3D view button or the full-featured 3D viewer button near the bottom of a static molecular graphic to load an interactive view."></TD>
|
||
<TD valign="top"><img SRC="../../IMG/spacer.gif" width="25" height="1" border="0" align="right"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>
|
||
The <B>molecular graphic</B> shows a snapshot of the 3D structure that can be viewed either as a <A HREF="#MolecularGraphicStatic"><B>static image</B></A>, or as an <A HREF="#MolecularGraphicInteractive"><B>interactive display</B></A>, as described below:<!-- I>(The <A HREF="#MmdbsrvThumbnailInteractionsSchematic">interactions schematic</A> beside the molecular graphic is a clickable cartoon that can be used to view more information about the molecular components, or <B>highlight molecules of interest</B> in both the schematic and the molecular graphic. The <A HREF="#InteractionsSchematicActions">actions taken by the interactions schematic</A> depend on whether you are looking at the static or interactive version of the molecular graphic.)</I -->
|
||
|
||
<UL>
|
||
<LI><A NAME="MmdbsrvMolecularGraphicStatic"></A><A NAME="MolecularGraphicStatic"></A><A NAME="MmdbsrvMolecularGraphicBiologicalForm"></A><A NAME="MmdbsrvThumbnailMolecularGraphicBiologicalForm"></A><B>STATIC IMAGE:</B> Upon first opening a <A HREF="#SummaryPage">structure summary page</A>, the molecular graphic shows a <!-- A HREF="#ThumbnailImageConservedDomainRecord"><B>*</B></A --> static image of the 3D structure<!--, generated by the <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> program -->.
|
||
The static image generally shows the default <A HREF="#DataProcessingBiologicalForms"><B>biological unit</B></A> of the structure.</LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="MmdbsrvMolecularGraphicInteractive"></A><A NAME="MolecularGraphicInteractive"></A>
|
||
<A NAME="MmdbsrvMolecularGraphicSpinIcon"></A>
|
||
<A NAME="MolecularGraphicSpinIcon"></A>
|
||
<A NAME="SpinIcon"></A>
|
||
<A NAME="MmdbsrvMolecularGraphic3DViewButton"></a>
|
||
<A NAME="MolecularGraphic3DViewButton"></a>
|
||
<A NAME="3DViewButton"></a>
|
||
<SPAN style="background-color: #FFFF00">Click the <!-- B>"3D view" button</B --> <IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_button_3d_view.png" width="57" height="19" border="0" alt="3D view"> button</SPAN> in the lower left corner of the static image to load an interactive view that uses <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A> ("I see in 3D"), NCBI's web-based 3D structure viewer.</LI>
|
||
|
||
<LI>The interactive display will load only if your web browser supports <a href="https://get.webgl.org/"><B>WebGL</B></a>. If it doesn't, the <B>static image</B> will be shown instead. To see the interactive view, modify the settings in your web browser to enable WebGL, or, if needed, update your web browser to a newer version that supports WebGL. (See the <a href="https://get.webgl.org/">WebGL</a> site for more information about compatibility with various web browsers.)</LI>
|
||
|
||
<LI>The <a href="#InteractionsSchematicActions">actions that happen when you mouseover or click on a node of the <SPAN style="background-color: #FFFF00">corresponding interactions schematic (described below)</a></SPAN> depend upon whether the MMDB summary page is displaying the the static or interactive version of the <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A>.</LI>
|
||
|
||
<!-- LI>If the structure contains <A HREF="#DataProcessingBiologicalFormsTypeClassification">multiple biological units</A> and you choose to <A HREF="#MmdbsrvDisplayOptions">display</A> "all biological units," then the MMDB summary page for the structure will show a molecular graphic (and corresponding <A HREF="#MmdbsrvThumbnailSchematic">interactions schematic</A>) for each biological unit.</LI -->
|
||
|
||
<!-- LI>If the structure contains <A HREF="#DataProcessingBiologicalFormsTypeClassification">two or more unique biological units</A>, then the default MMDB summary page for the structure displays a molecular graphic (and corresponding schematic cartoon) for each one, providing a non-redundant view of the biological units that have been detected within the asymmetric unit of the structure record.><LI -->
|
||
|
||
<!-- LI><A NAME="MmdbsrvThumbnailMolecularGraphicAsymmetricUnit"></A>
|
||
A view of the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> is also available, if desired.</LI -->
|
||
|
||
<!-- LI><I>Note</I>: [As of May 2011]The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records resolved by x-ray crystallography or neutron diffraction of crystals. In such cases, you will see the same molecular graphic in all three <A HREF="#MmdbsrvDisplayOptions">display options</A> (i.e., unique biological units = all biological units = asymmetric unit). In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>, or it represents multiple copies of the biological unit. In those cases, the biological unit displays will be different from the asymmetric unit display.</LI -->
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<!-- LI><A NAME="_____"></A>
|
||
<B>Click</B> on the molecular graphic to open an interactive view of the structure in the free <a href="../../CN3D/cn3d.shtml"><B>Cn3D</B></a> program. If you click on the thumbnail for the asymmetric unit, Cn3D will display the structure as it was deposited by the author. If you click on the thumbnail for a specific biological unit within the structure, Cn3D will display only that biological unit. Note that Cn3D must be installed on your computer and configured as a helper application for your browser in order for this function to work. If you already have Cn3D 4.1 or ealier on your computer, you will need to upgrade to <B>Cn3D 4.3</B> (<A HREF="../../CN3D/cn3dinstall.shtml">install</A>) in order to view biological units that were reconstructed by applying transformations from <A HREF="#DataProcessingCrystalSymmetry">crystallographic symmetry</A> or by <A HREF="#DataProcessingBiologicalFormsMergeSplitFiles">merging PDB split files</A>.[{{Only data for the portion of the structure that was shown in the thumbnail will appear in the Cn3D view. If you'd like to open a view of the data set that was provided by the submitter in the source PDB record, click on the thumbnail for the asymmetric unit.}}]<[<A HREF="../../CN3D/cn3dinstall.shtml">Download</A> that free program (available for PC, Mac, or Unix) before clicking on the image, if it is not yet on your computer.]</LI -->
|
||
|
||
<LI><B>INTERACTIVE DISPLAY</B>: Once the interactive view loads, you can:</LI><BR>
|
||
|
||
<UL>
|
||
<LI><B>Click on the structure to stop the spin.</B></LI>
|
||
<LI><B>Click an icon</B> in the corresponding <a href="#MmdbsrvThumbnailInteractionsSchematic"><B>interactions schematic</B></a> <!-- (that appears beside the molecular graphic in the <A HREF="#SummaryPage">structure summary page</A>) --> to highlight molecule in both the schematic and the molecular graphic.</LI>
|
||
<LI><B>Right click</B> on the structure to open a <B>menu</B> that allows you to control various aspects of the display (background color, display solvent accessible surface) and/or to "export image."</LI>
|
||
<LI>If you select "<B>Export Image</B>" from the menu, the molecular graphic will open in a separate window. In that separate window, you can right click on the exported image to use the browser's "<B>save image as</B>" function.</LI>
|
||
<!-- UL>
|
||
<LI>Right click on the exported image to use the browser's "<B>save image as</B>" function.</LI>
|
||
<LI><B>Reload</B> the <a href="#SummaryPage">MMDB summary page</a> to reveal the "3D view" button again, then <B>repeat</B> the process as many times as desired in order to save snapshots of the structure at the desired angles.</LI>
|
||
<LI>Each time you select "Export Image," a separate window will open, making it possible to <B>view the structure from many angles simultaneously</B>.</LI>
|
||
</UL -->
|
||
<LI><B>Reload</B> the <a href="#SummaryPage">MMDB summary page</a> to refresh the page and to reveal the "3D view" button again. Then <B>repeat</B> the steps above as many times as desired in order to save snapshots of the structure at the desired angles.</LI>
|
||
<LI>Each time you select "Export Image," a new, separate window will open, making it possible to <B>view the structure from many angles simultaneously</B>.</LI>
|
||
<!-- LI>Click the <IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_icon_expand_view.png" WIDTH="20" HEIGHT="20" BORDER="0" ALT="icon that launches full feature iCn3D in another window"> icon to <B>open an larger view of the structure</B>, which will occupy 95% of the browser window's height or width, whichever is larger.</LI -->
|
||
<!-- LI><SPAN style="background-color: #FFFF00">Click the <IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_icon_launch_full_feature_icn3d.png" WIDTH="20" HEIGHT="20" BORDER="0" ALT="icon that launches full feature iCn3D in another window"> icon</SPAN> to <B>launch the advanced (full feature) version of iCn3D</B> in another window. The full feature version provides many additional controls for rendering, labeling, coloring, and saving the structure, as well as viewing corresponding sequence data.</LI -->
|
||
</UL><BR>
|
||
|
||
<LI>
|
||
<A NAME="MmdbsrvMolecularGraphicLaunchIcon"></A>
|
||
<A NAME="MolecularGraphicLaunchIcon"></A>
|
||
<A NAME="LaunchIcon"></A>
|
||
<A NAME="MmdbsrvMolecularGraphicFullFeatured3DViewerButton"></A>
|
||
<A NAME="MolecularGraphicFullFeatured3DViewerButton"></A>
|
||
<A NAME="FullFeatured3DViewerButton"></A>
|
||
<B>LAUNCH FULL iCn3D</B>: <SPAN style="background-color: #FFFF00">Click the <IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_button_full_featured_3d_viewer.png" WIDTH="150" HEIGHT="19" BORDER="0" ALT="full-featured 3D viewer"> button</SPAN> to launch the advanced (full feature) version of <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A> in another window.</LI><BR>
|
||
|
||
<UL>
|
||
<LI> The full feature version provides many additional controls for rendering, labeling, coloring, and saving the structure, as well as viewing corresponding sequence data.</LI><BR>
|
||
<LI>Note that iCn3D will launch only if your web browser supports <a href="https://get.webgl.org/"><B>WebGL</B></a>. If it doesn't, modify the settings in your web browser to enable WebGL, or, if needed, update your web browser to a newer version that supports WebGL. (See the <a href="https://get.webgl.org/">WebGL</a> site for more information about compatibility with various web browsers.)</LI>
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
<A HREF="#MmdbsrvStructureView"><B>Additional structure viewing options:</B></A> The "Download Structure Data" dialog box (that appears to the right of the molecular graphic on the <A HREF="#SummaryPage">structure summary page</A>) provides options for downloading the structure data in a variety of <A HREF="#MmdbsrvStructureViewFileFormat">file formats</A>. The ASN.1 format, for example, can be interactively viewed in <A HREF="../../CN3D/cn3d.shtml"><B>Cn3D</B></A>, NCBI's free 3D structure viewing application, which provides a wide range of options for rendering, labeling, coloring, annotating, viewing sequence data, and more.<!-- The free <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> program (available for PC, Mac, or Unix) must be present on your computer in order for this to work. --> <a HREF="/Structure/CN3D/cn3dinstall.shtml">Installation</a> takes only a couple of minutes and a <a HREF="/Structure/CN3D/cn3dtut.shtml"><B>tutorial</B></a> describes the program's features and functions.<BR><BR>
|
||
<A HREF="#MmdbsrvSave3dView"><B>Additional options for saving images of 3D structures</B></A> are also available, and are described in a separate section of this document.<BR><BR>
|
||
|
||
<!-- ====== ADDITIONAL_THUMBNAIL_IMAGES_IN_CDD ========= -->
|
||
|
||
<A NAME="ThumbnailImageConservedDomainRecord"></A>
|
||
<!-- B>*</B> <I>A separate thumbnail image is provided for each protein molecule in the graphical summary of <A HREF="#MmdbsrvMolecularComponents">molecular components</A>; it opens a view of the 3D structure that colors the specific protein molecule (or its 3D domains, if present) within the overall structure. In addition, specially annotated images of the structure might be available in the <A HREF="../../cdd/cdd.shtml">Conserved Domain Database (CDD)</A>, if the structure has been incorporated into an <A HREF="../../cdd/cdd_help.shtml#CDSource_NCBI_curated">NCBI-curated</A> domain record. As noted in the section on "<A HREF="#DatabaseApplications">How can 3D structures be used to learn more about proteins and other biomolecules?</A>", curators of that database combine information about conserved domains from multiple sequence alignments with what we can infer from three-dimensional structure and three-dimensional structure superposition, in order to aid understanding of sequence/structure/function relationships. As a result, the NCBI-curated conserved domain records include representations of <A HREF="../../cdd/cdd_help.shtml#NCBI_curated_domains">conserved structural core motifs</A> whenever possible, and the 3D structure images in the domain's <A HREF="../../cdd/cdd_help.shtml#ConservedFeatures">conserved feature</A> summary box link to <A HREF="../../cdd/cdd_help.shtml#CDStructure">specially annotated views of the 3D structures</A> that highlight the conserved feature.</I -->
|
||
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="3" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="200"><A NAME="MmdbsrvThumbnailSchematic"></A><A NAME="InteractionsSchematic"></A><A NAME="MmdbsrvThumbnailInteractionsSchematic"></A><A NAME="MmdbsrvThumbnailSchematicInteractions"></A><A NAME="MmdbsrvInteractionsSchematic"></A><A NAME="MmdbsrvThumbnailInteractions"></A><A NAME="MmdbsrvThumbnailSchematic"></A><A NAME="MmdbsrvInteractionPopup"></A><B>Interactions Schematic</B><BR><BR><IMG SRC="images/1PTH_interactions_schematic.png" WIDTH="150" HEIGHT="150" BORDER="1" ALT="Sample interactions schematic for sheep prostaglandin H2 sythase, from the 1PTH structure record."></TD>
|
||
<TD valign="top" align="left"><img SRC="../../IMG/spacer.gif" width="25" height="1" border="0" align="right"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top of document"></A>The <B>interactions schematic</B> shows the <A HREF="#MmdbsrvMolecularComponents">molecular components</A> of the <A HREF="#DataProcessingBiologicalForms">biological unit</A> and the <A HREF="#DataProcessingInteractions">interactions</A> among them. <I>(Note: Structures that only have alpha carbons, and no side chains, do not show interactions. In those cases, the schematic just shows the structure's molecular components (proteins, nucleotide sequences, and ligands) as free floating (disconnected) icons.)</I><BR><BR>
|
||
|
||
The schematic is <B>clickable</B>, and <SPAN style="background-color: #FFFF00">the <a href="#InteractionsSchematicActions">actions that happen when you mouseover or click on a node (described below)</a></SPAN> depend upon whether the MMDB summary page is displaying the the static or interactive version of the <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A>.
|
||
<!-- a href="#InteractionsSchematicActionsStatic">static molecular graphic</A> or the <a href="#InteractionsSchematicActionsInteractive">interactive molecular graphic</A --><!-- I>(This schematic is not shown if you choose to <A HREF="#MmdbsrvDisplayOptions">display</A> the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>.)</I -->
|
||
|
||
<UL>
|
||
<LI><A NAME="MmdbsrvThumbnailSchematicMolecularComponents"></A>The <!-- A HREF="#MmdbsrvMolecularComponents" --><B>molecular components</B> of the biological unit can include the following:<BR><BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" CLASS="NormalText" CELLPADDING="0">
|
||
|
||
<TR>
|
||
<TD WIDTH="430" ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvProteins">Proteins</A>, if present, are shown as circles:</TD>
|
||
<TD WIDTH="80" ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvProteins"><IMG SRC="images/molecular_component_protein_circle.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="example of circle icons used to depict proteins"></A>  etc.</TD>
|
||
<TD ALIGN="LEFT" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="3"><img SRC="../../IMG/spacer.gif" width="15" height="4" border="0"></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="430" ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvNucleotides">Nucleotide sequences</A> (DNA, RNA), if present, are shown as squares:</TD>
|
||
<TD WIDTH="80" ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvNucleotides"><IMG SRC="images/molecular_component_nucleotide_square.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="example of square icons used to depict nucleotide sequences"></A>  etc.</TD>
|
||
<TD ALIGN="LEFT" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="3"><img SRC="../../IMG/spacer.gif" width="15" height="4" border="0"></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="430" ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvChemicals">Chemicals</A>, if present, are shown as diamonds:</TD>
|
||
<TD WIDTH="80" ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvChemicals"><IMG SRC="images/molecular_component_chemical_diamond.png" WIDTH="38" HEIGHT="15" BORDER="0" ALT="example of diamond shaped icons used to depict chemicals"></A> etc.</TD>
|
||
<TD ALIGN="LEFT" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="3"><img SRC="../../IMG/spacer.gif" width="15" height="4" border="0"></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="430" ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvNonStandardBiopolymers">Non-standard biopolymers</A>, if present, are shown as parallelograms:<br>
|
||
(These are molecules such as nucleotide or protein sequences that contain a large percentage of non-standard residues.)</TD>
|
||
<TD WIDTH="80" ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvNonStandardBiopolymers"><IMG SRC="images/molecular_component_other_non_standard_biopolymers_parallelogram.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="example of parallelogram icons used to depict non-standard biopolymers"></A>  etc.</TD>
|
||
<TD ALIGN="LEFT" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="3"><img SRC="../../IMG/spacer.gif" width="15" height="4" border="0"></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="3">If any protein or nucleotide molecules in the structure were generated by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry"><B>crystallographic symmetry</B></A>, their labels are shown as alphanumeric combinations (for example, <IMG SRC="images/molecular_component_protein_circle_crystal_symmetry.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="Example of circle icons with alphanumeric labels used to depict protein molecules generated by applying transformations from crystallographic symmetry."> or <IMG SRC="images/molecular_component_nucleotide_square_crystal_symmetry.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="Example of square icons with alphanumeric labels used to depict nucleotide sequences generated by applying transformations from crystallographic symmetry.">), indicating the source molecule from which they were generated (to the left of the <b>underscore bar</b>) and the copy number (to the right of the underscore bar). Chemicals that interact only with such molecules were also generated by applying transformations from crystallographic symmetry; their icon labels also include an underscore bar, with a number on either side of the underscore bar to indicate the source chemical and the copy number, respectively.</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
The protein and nucleotide icons are <B>scaled to show the relative sizes</B> of those molecular components, so they are roughly comparable to each other based on molecular weight. All chemical icons are the same size.<BR><BR>
|
||
</LI>
|
||
|
||
<LI><A HREF="#DataProcessingInteractions"><B>Interactions</B></A> <B>among components</B> are shown as <B>lines</B>, and an interaction is displayed only if there are <A HREF="#DataProcessingInteractionsContactNumberThreshold">at least 5 contacts</A> at a distance of <A HREF="#DataProcessingInteractionsDistanceThreshold">4 Å or less</A> between the heavy atoms of the molecules.<!-- Å is the HTML code for Angstrom, <20> --></LI><BR>
|
||
|
||
<UL>
|
||
<LI>There is no meaning to the length of the lines in the interaction schematic. After the interactions are drawn, the diagram is flattened out to fit into the square, lengthening or shortening lines as needed.</LI><BR>
|
||
|
||
<LI>Because of the latter thresholds, <B>ions</B> that are part of the biological unit may be missing from the interaction diagram, but they will be listed in the table of <A HREF="#MmdbsrvMolecularComponents">molecular components and interactions</A>. Interactions for short peptides, or for molecule types other than protein, DNA/RNA, and chemical, are not calculated. Molecules, such as crystallization agents, etc., that are not part of the biologically active molecule are absent from both the interaction schematic and the molecular components list.</LI><BR>
|
||
</UL>
|
||
|
||
<LI>If the structure contains <A HREF="#DataProcessingBiologicalFormsTypeClassification">multiple biological units</A> and you choose to <A HREF="#MmdbsrvDisplayOptions">display</A> "all biological units," then the MMDB summary page for the structure will show a schematic cartoon (and corresponding <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A>) for each one.<!-- providing a non-redundant view of the biological units {{unique biological units}} that have been detected within the asymmetric unit of the structure record. --></LI>
|
||
|
||
<!-- LI>3/23/2011<I>* Note: There is no meaning to the length of the lines in the interaction schematic. After the interactions are drawn, the diagram is flattened out to fit into the square, lengthening or shortening lines as needed. The protein (circle) and nucleotide (square) icons are scaled to show the relative sizes of those molecular components, and there can be 4 different sizes. A content scaling factor makes the protein and nucleotide icons more or less comparable to each other based on molecular weight. No node in an interaction diagram can be 2X as large as the other. Chemical (diamond) icons are all the same size.</I></LI -->
|
||
|
||
<!-- LI> If you choose to view the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A>, the page will display <I>only</I> a molecular graphic. Instead of displaying the schematic cartoon, a note will appear in its place describing the relationship between the asymmetric unit and the biological unit(s).</LI -->
|
||
|
||
</UL>
|
||
|
||
<A NAME="MmdbsrvThumbnailSchematicActions"></A><A NAME="MmdbsrvThumbnailInteractionsSchematicActions"></A><A NAME="MmdbsrvThumbnailSchematicInteractionsActions"></A><A NAME="InteractionsSchematicActions"></A>
|
||
<SPAN style="background-color: #FFFF00"><B>The actions taken by the interactions schematic</B> when you click on a node depend on whether the <B>static</B> or <B>interactive</B> version of the <A HREF="#MmdbsrvThumbnailMolecularGraphic"><B>molecular graphic</B></A> is displayed on the page.</SPAN>.
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="InteractionsSchematicActionsStatic"></A>If the <B>static molecular graphic</B></A> is displayed:</LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><B>Mouse over</B> any node in the interactions schematic to view the molecule name.<!-- {{To open a detailed view of the interactions between that molecule and others, follow the "<B>explore interactions</B>" link for that molecule in the table of <A HREF="#MmdbsrvMolecularComponents">molecular components</A>.}} --></LI><BR>
|
||
|
||
<LI><B>Double click</B> on a node in the interaction schematic to jump down to the corresponding part of the <A HREF="#MmdbsrvMolecularComponents">Molecules and Interactions</A> table, which provides additional information about the molecule.</LI>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="InteractionsSchematicActionsInteractive"></A>If the <B>interactive molecular graphic</B></A> is displayed:</LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><B>Each node</B> in the interaction schematic works as a <B>toggle switch</B> to highlight a molecule on/off.</LI><BR>
|
||
|
||
<LI><B>Double click on a node</B> in the schematic to <B>highlight</B> just that molecule in the 3D structure.</LI><BR>
|
||
|
||
<LI><B>Double click on that molecule again</B> in the interaction schematic to <B>un-highlight</B> the molecule and revert to the previous view of the 3D structure.</LI><BR>
|
||
|
||
<!-- LI>To <B>highlight more than one molecule</B>, press the <B>Control key</B> (on a PC) or the <B>Command key</B> (on a Mac) while you click on the molecules of interest</LI><BR -->
|
||
|
||
<LI>To <B>highlight all molecules of the same type</B>, click on the term "<B>protein</B>," "<B>nucleotide</B>," or "<B>chemical</B>" that appears at the bottom of the interactions schematic. (Click on the term again to toggle the highlight off, if desired.)</LI>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD colspan="3" valign="top" class="MiniText"> </TD>
|
||
</TR -->
|
||
|
||
<!-- TR>
|
||
<TD colspan="3" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" width="150"><A NAME="MmdbsrvThumbnailImageProteinMolecule"><B>Thumbnail image for an individual protein molecule</B></A></TD>
|
||
<TD valign="top" align="left" colspan="2">Text text text text text text text text text text text text text text text text text text text text text text text text text text text text.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="150" valign="top" align="left"> </TD>
|
||
<TD width="200" valign="top" align="left"><A NAME="_________"></A><LI><B>_______</B></LI></TD>
|
||
<TD valign="top" align="left">_____________________________________________</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="150" valign="top" align="left"> </TD>
|
||
<TD width="200" valign="top" align="left"><A NAME="_________"></A><LI><B>_______</B></LI></TD>
|
||
<TD valign="top" align="left">_____________________________________________</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ========= MMDBSRV_DOWNLOAD_STRUCTURE_DATA_OPTIONS=========== -->
|
||
|
||
<A NAME="MmdbsrvDownloadStructureData"></A>
|
||
<A NAME="DownloadStructureData"></A>
|
||
<A NAME="MmdbsrvStructureView"></A>
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Download Structure Data (save 3D structure record)</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<!-- ========= MINI_TOC FOR DOWNLOAD_STRUCTURE_DATA_OPTIONS =========== -->
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormat"><B>Format</B></A>:
|
||
<A HREF="#MmdbsrvStructureViewFileFormatCn3D">Cn3D</A>,
|
||
<A HREF="#MmdbsrvStructureViewFileFormatPDB">PDB</A>,
|
||
<A HREF="#MmdbsrvStructureViewFileFormatXML">XML</A>,
|
||
<A HREF="#MmdbsrvStructureViewFileFormatJSON">JSON</A>,
|
||
<A HREF="#MmdbsrvStructureViewFileFormatPNG">PNG (image)</A></LI>
|
||
|
||
<!-- LI><A HREF="#MmdbsrvStructureViewDisplayAs"><B>Display as</B></A>:
|
||
<A HREF="#MmdbsrvStructureView3DStructure">3D Structure</A>,
|
||
<A HREF="#MmdbsrvStructureViewSeeFile">see file</A>,
|
||
<A HREF="#MmdbsrvStructureViewSaveFile">save file</A></LI -->
|
||
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSet"><B>Data set</B></A>:
|
||
<A HREF="#MmdbsrvStructureViewDataSetAllAtoms">single 3D structure</A>,
|
||
<A HREF="#MmdbsrvStructureViewDataSetAllModels">all 3D structures</A>,
|
||
<A HREF="#MmdbsrvStructureViewDataSetBackbone">alpha carbons</A>,
|
||
<A HREF="#MmdbsrvStructureViewDataSetPDBdataset">PDB source file</A></LI>
|
||
|
||
<LI><A HREF="#MmdbsrvSave"><B>Additional details</B></A>:
|
||
<A HREF="#DownloadStructureDataIllustration"><span style="color:#d70000"><I>annotated illustration</I></span> of download options</A>,<BR>
|
||
<A HREF="#MmdbsrvSaveDataFile">details about data saved in each file format</A>: <A HREF="#MmdbsrvSaveASN1format">ASN.1 (Cn3D)</A>,
|
||
<A HREF="#MmdbsrvSavePDBformat">PDB</A>,
|
||
<A HREF="#MmdbsrvSaveXMLformat">XML and JSON</A>,<BR>
|
||
<A HREF="#MmdbsrvSave3dView">save image of 3D structure</A>,
|
||
<A HREF="#MmdbsrvSaveComponents">save structure components</A></LI>
|
||
|
||
<!-- LI><A HREF="#MmdbsrvStructureViewURLformat"><B>Web API: URL format for displaying or saving a structure record</B></A>:<BR>
|
||
<A HREF="#StructureViewURLformatBaseURL">base URL</A>,
|
||
<A HREF="#StructureViewURLformatParameters">parameters and allowable values</A>,
|
||
<A HREF="#StructureViewURLformatExamples">examples of URLs for displaying or saving 3D structure records</A></LI -->
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ======== END_MINI_TOC FOR DOWNLOAD_STRUCTURE_DATA_OPTIONS ========= -->
|
||
|
||
|
||
<!-- ===== DOWNLOAD_STRUCTURE_DATA_OPTIONS: FILE_FORMAT_and_DATASET ==== -->
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<!-- ======== DOWNLOAD_STRUCTURE_DATA_OPTIONS: FILE_FORMAT ======== -->
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"><A NAME="MmdbsrvStructureViewFileFormat"></A><A NAME="MmdbsrvStructureViewProgram"></A><B>Format</B></TD>
|
||
<TD valign="top" align="left" colspan="2">The <B>"Format" options</B> that you select in the "Download Structure Data" box of an <A HREF="#SummaryPage">MMDB summary page</A> will <B>act upon the</B> <A HREF="#MmdbsrvDisplayOptions">biological unit(s) or asymmetric unit currently displayed</A> in your browser window. <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD colspan="4" valign="top" class="TableText1">
|
||
<BLOCKQUOTE>
|
||
The "<B>Format</B>" options that you select in the "Download Structure Data" box of an MMDB summary page will <B>act upon the</B> <A HREF="#MmdbsrvDisplayOptions"><B>biological unit(s) or asymmetric unit currently displayed</B></A> in your browser window.
|
||
</BLOCKQUOTE>
|
||
</TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewFileFormatCn3D"></A><A NAME="MmdbsrvStructureViewInCn3D"></A><A NAME="MmdbsrvStructureViewFileFormatASN1"></A><LI><B>ASN.1 (Cn3D)</B></LI></TD>
|
||
<TD valign="top" align="left">Renders the structure data in <A HREF="../../asn1.html"><B>ASN.1 file format</B></A>, which can be used to display the 3D structure in NCBI's free <a href="../../CN3D/cn3d.shtml"><B>Cn3D</B></a> structure-viewing program. Cn3D allows examination of <A HREF="#DataProcessingBiologicalForms">biological units</A>, <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric units</A>, and <A HREF="#DatabaseApplications">sequence-structure relationships</A>, and allows <A HREF="#EvolutionaryRelationships">superposition</A> of geometrically similar structures.<BR><BR>
|
||
|
||
The data will either be for an individual <A HREF="#DataProcessingBiologicalForms">biological unit</A> or for the <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, depending on what you chose to <A HREF="#MmdbsrvDisplayOptions">display</A> on the <A HREF="#SummaryPage">MMDB summary page</A> when you pressed the "<A HREF="#MmdbsrvStructureView">download</A>" button.<BR><BR>
|
||
|
||
The structure can be opened automatically in Cn3D, if Cn3D has been <a HREF="/Structure/CN3D/cn3dinstall.shtml">installed</a> on your computer, and if your browser has been <A HREF="../../CN3D/cn3dinstall.shtml#browser">configured</A> to use it as a helper app.<BR><BR>
|
||
|
||
Cn3D is available for Windows, Macintosh, and Unix platforms. <a HREF="/Structure/CN3D/cn3dinstall.shtml">Installation</a> takes only a couple of minutes and a <a HREF="/Structure/CN3D/cn3dtut.shtml"><B>tutorial</B></a> describes the program's features and functions.<!-- The Cn3D installation page also describes how to <A HREF="../../CN3D/cn3dinstall.shtml#browser">configure your browser</A> to use Cn3D as a helper app, and to launch it automatically when the "Cn3D" option is selected in combination with the "<A HREF="#MmdbsrvStructureViewTasks3DStructure">3D structure</A>" option from the "<A HREF="#MmdbsrvStructureViewTasks">Display As</A>" menu. --><BR>
|
||
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewFileFormatPDB"></A><A NAME="MmdbsrvStructureViewInRasmol"></A><LI><B>PDB</B></LI></TD>
|
||
<TD valign="top" align="left">Renders the structure data in <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format"><B>PDB file format</B></A>, which can be used to display the 3D structure with <A HREF="http://www.umass.edu/microbio/rasmol/">Rasmol</A> or other viewers that can read that format.<BR><BR>
|
||
|
||
The data will either be for an individual <A HREF="#DataProcessingBiologicalForms">biological unit</A> or for the <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, depending on what you chose to <A HREF="#MmdbsrvDisplayOptions">display</A> on the <A HREF="#SummaryPage">MMDB summary page</A> when you pressed the "<A HREF="#MmdbsrvStructureView">download</A>" button.<BR><BR>
|
||
|
||
Note, however, that the saved file may be somewhat different from the original <A HREF="#SourceDatabases">PDB source file</A>, due to content validation procedures applied during <A HREF="#DataProcessing">MMDB data processing</A>. The differences are explained in a separate section of this document on "<A HREF="#MmdbsrvSave">additional details about structure data download options</A> > <A HREF="#MmdbsrvSavePDBformat">PDB format</A> > <A HREF="#MmdbsrvSavePDBformatDetails">details about the data that are saved</A>."<BR><BR>
|
||
|
||
<I>To save the original <A HREF="#SourceDatabases">PDB source file</A>, click on the "Download" button that appears next to the <A HREF="#MmdbsrvPDBID">PDB ID</A> in the upper right hand corner of the <A HREF="#SummaryPage">structure summary page</A>."</I>
|
||
<!-- To save an exact copy of the original <A HREF="#SourceDatabases">PDB source file</A>, display the <A HREF="#AsymmetricUnit">asymmetric unit</A> and select "File Format: PDB" + "<A HREF="#MmdbsrvStructureViewDataSet">Data Set</A>: <A HREF="#MmdbsrvStructureViewDataSetPDBdataset">PDB data set</A>." -->
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewFileFormatXML"></A><LI><B>XML</B> <!-- A HREF="#NoteSaveRecord">†</A --></LI></TD>
|
||
<TD valign="top" align="left">
|
||
Renders the data in <A HREF="/IEB/ToolBox/XML/ncbixml.txt"><B>XML file format</B></A>. The data will either be for an individual <A HREF="#DataProcessingBiologicalForms">biological unit</A> or for the <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, depending on what you chose to <A HREF="#MmdbsrvDisplayOptions">display</A> on the <A HREF="#SummaryPage">MMDB summary page</A> when you pressed the "<A HREF="#MmdbsrvStructureView">download</A>" button.<!-- This option is valid only when the "<A HREF="#MmdbsrvStructureViewFileFormat">format</A>" menu is set to "ASN.1 (Cn3D)" (which is the <A HREF="../../asn1.html">ASN.1</A> file format used by NCBI's free <A HREF="../../CN3D/cn3d.shtml">CN3D</A> structure viewing application). A separate section of this document provides <A HREF="#MmdbsrvSave">additional details about structure data download options</A> and what data are saved in each case</A>.[<A HREF="#MmdbsrvSave"><span style="color:#d70000">illustration</span></A>] --></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewFileFormatJSON"></A><LI><B>JSON</B> <!-- A HREF="#NoteSaveRecord">†</A --></LI></TD>
|
||
<TD valign="top" align="left">
|
||
Renders the data in <A HREF="http://json.org/"><B>JSON file format</B></A>. The data will either be for an individual <A HREF="#DataProcessingBiologicalForms">biological unit</A> or for the <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, depending on what you chose to <A HREF="#MmdbsrvDisplayOptions">display</A> on the <A HREF="#SummaryPage">MMDB summary page</A> when you pressed the "<A HREF="#MmdbsrvStructureView">download</A>" button.<!-- This option is valid only when the "<A HREF="#MmdbsrvStructureViewFileFormat">format</A>" menu is set to "ASN.1 (Cn3D)" (which is the <A HREF="../../asn1.html">ASN.1</A> file format used by NCBI's free <A HREF="../../CN3D/cn3d.shtml">CN3D</A> structure viewing application). A separate section of this document provides <A HREF="#MmdbsrvSave">additional details about structure data download options</A> and what data are saved in each case</A>.[<A HREF="#MmdbsrvSave"><span style="color:#d70000">illustration</span></A>] --></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewInJMol"></A><LI><B>JMol</B></LI></TD>
|
||
<TD valign="top" align="left">The "JMol" option [setting, when used in combination with the "<A HREF="#MmdbsrvStructureViewTasksDisplay"><B>display</B></A>" option from the <A HREF="#MmdbsrvStructureViewTasks">Tasks</A> menu,] opens an interactive display of the 3-D structure with [<A HREF="http://jmol.sourceforge.net/">]<A HREF="http://www.jmol.org/ ">Jmol</A> (an open-source Java viewer for chemical structures in 3D) or other viewers that can read <A HREF="________">{{___ format}}</A>.
|
||
When the "JMol" option is selected in combination with the "<A HREF="#MmdbsrvStructureViewTasksSaveFile"><B>save file</B></A>" option from the <A HREF="#MmdbsrvStructureViewTasks">Tasks</A> menu, the data will be saved in <A HREF="________">{{___ format}}</A>.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> <BR> </TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewFileFormatPNG"></A><LI><B>PNG (image)</B> <!-- A HREF="#NoteSaveRecord">†</A --></LI></TD>
|
||
<TD valign="top" align="left">
|
||
Saves the <B>default view</B> of the structure in <A HREF="http://www.w3.org/TR/PNG/"><B>PNG file format</B></A>.<BR><BR>
|
||
|
||
<!-- If you prefer to save the structure from a <B>viewing angle that is different from the default</B>, and/or control display elements such as background color, termini labels, and solvent accessible surface:<BR>
|
||
|
||
<UL>
|
||
<LI>Click the 3D view button <IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_button_3d_view.png" WIDTH="57" HEIGHT="19" BORDER="0" ALT="3D view button that loads an interactive view of the 3D structure"> in the lower left hand corner of the static <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A> to load the interactive view of the structure in <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A>, NCBI's web-based viewer for 3D structures (see <A HREF="#MmdbsrvSave"><span style="color:#d70000"><I>annotated illustration</I></span></A>). Note that the interactive view will load only if your browser supports <A HREF="https://get.webgl.org/">WebGL</A>.</LI>
|
||
<LI> Once the structure spins to the desired position, click on the structure to stop the spin.</LI>
|
||
<LI>Right click to open a menu that allows you to control various aspects of the display and/or to "export image."</LI>
|
||
<LI>Select "export image" to open the view in a separate window.</LI>
|
||
<LI>Right click on the exported image to use the browser's "save image as" function.</LI>
|
||
<LI>Reload the page to reveal the 3D view button again, then repeat the process as many times as desired in order to save snapshots of the structure at various angles.</LI>
|
||
<LI>If desired, click the <IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_icon_launch_full_feature_icn3d.png" WIDTH="20" HEIGHT="20" BORDER="0" ALT="icon that launches full feature iCn3D in another window"> icon to "launch full feature iCn3D in another window" for additional viewing and save options.</LI>
|
||
</UL -->
|
||
|
||
The image saved will either be for an individual <A HREF="#DataProcessingBiologicalForms">biological unit</A> or for the <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, depending on what you chose to <A HREF="#MmdbsrvDisplayOptions">display</A> on the <A HREF="#SummaryPage">MMDB summary page</A> when you pressed the "<A HREF="#MmdbsrvStructureView">download</A>" button.<BR><BR>
|
||
|
||
<I>Separate sections of this document provide an <A HREF="#MmdbsrvSave">additional details about structure data downloads</A> and <A HREF="#MmdbsrvSave3dView">additional options for saving images of 3D structures</A>.
|
||
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD width="120" valign="top" class="NormalText"> </TD>
|
||
<TD colspan="3" valign="top" class="NormalText"><I>Separate sections of this document provide an <A HREF="#DownloadStructureDataIllustration">annotated illustration of download options</A>; <A HREF="#MmdbsrvSaveDataFile">details about data saved</A> in the following file formats: (<A HREF="#MmdbsrvSaveASN1format">ASN.1 (Cn3D)</A>, <A HREF="#MmdbsrvSavePDBformat">PDB</A>, <A HREF="#MmdbsrvSaveXMLformat">XML and JSON</A>); <A HREF="#MmdbsrvSave3dView">additional options for saving images of 3D structures</A>, and instructions for <A HREF="#MmdbsrvSaveComponents">saving structure components</A>.</I></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR -->
|
||
|
||
<!-- ======== END_DOWNLOAD_STRUCTURE_DATA_OPTIONS: FILE_FORMAT ======== -->
|
||
|
||
<!-- ========= OLD:DISPLAY_OPTIONS_STRUCTURE_VIEW_DISPLAY_AS_MENU ========== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" align="left" colspan="2"><A NAME="MmdbsrvStructureViewDisplayAs"></A><A NAME="MmdbsrvStructureViewTasks"></A><B>Display As</B> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
<TD valign="top" align="left"> </TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureView3DStructure"></A><A NAME="MmdbsrvStructureViewTasksDisplay"></A><LI><B>3D Structure</B></LI></TD>
|
||
<TD valign="top" align="left">Opens an interactive view of the 3D structure with a program that can accept the file format you have selected. If you have selected the <B>Cn3D format</B>, you can display the structure's <A HREF="#DataProcessingBiologicalForms">biological unit(s)</A> or <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A> [{{and in the case of <A HREF="#DataProcessingBiologicalFormsMergeSplitFiles">PDB split files</A>, you can display MMDB's merged file that shows the complete structure}}]. If you have selected the <B>PDB format</B>, you can display the structure's asymmetric unit in a program such as Rasmol or another 3D structure viewer that accepts the PDB format.<BR><BR>
|
||
<I>Note that the structure viewing <B>program</B> you will use (e.g., NCBI's free <a href="../../CN3D/cn3d.shtml"><B>Cn3D</B></a> program or a PDB-format compatible viewer) must be <A HREF="../../CN3D/cn3dinstall.shtml"><B>installed</B></A> on your computer and <B><A HREF="../../CN3D/cn3dinstall.shtml#browser"><B>configured</B></A> as a helper application</B> for your browser in order for the <B>"View Structure" button</B> to automatically open the 3D structure. If you already have Cn3D 4.1 or earlier on your computer, you will need to <B>upgrade to Cn3D 4.3</B> (<A HREF="../../CN3D/cn3dinstall.shtml">install</A>) in order to view 3D structures that were reconstructed by applying transformations from <A HREF="#DataProcessingCrystalSymmetry">crystallographic symmetry</A></I>[{{or by <A HREF="#DataProcessingBiologicalFormsMergeSplitFiles">merging PDB split files</A>}}].[{{which is packaged together with the <A HREF="../../cdtree/cdtree.shtml">CDTree</A> program (<A HREF="../../cdtree/cdtreeInstall.shtml">install</A>)}}]
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"></A><A NAME="MmdbsrvStructureViewSeeFile"></A><A NAME="MmdbsrvStructureViewTasksSeeFile"><LI><B>See File</B></LI></TD>
|
||
<TD valign="top" align="left">Displays the contents of the data file in the browser window, either in <B>Cn3D</B> <A HREF="../../asn1.html">(ASN.1) format</A> or [<A HREF="http://www.wwpdb.org/docs.html">]<A HREF="http://www.wwpdb.org/documentation/file-format"><B>PDB</B> format</A>, as determined by which "<A HREF="#MmdbsrvStructureViewFileFormat">File Format</A>" option you selected.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewSaveFile"></A><A NAME="MmdbsrvStructureViewTasksSaveFile"></A><LI><B>Save File</B> [<A HREF="#NoteSaveRecord">†</A>]</LI></TD>
|
||
<TD valign="top" align="left">
|
||
Saves data for an individual <A HREF="#DataProcessingBiologicalForms">biological unit</A> or for the <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A> (depending on what you have chosen to <A HREF="#MmdbsrvDisplayOptions">display</A>) to your local computer. Use the <A HREF="#MmdbsrvStructureViewFileFormat">file format</A> menu to specify the format in which the data should be saved: Cn3D (<A HREF="../../asn1.html">ASN.1) format</A> or [<A HREF="http://www.wwpdb.org/docs.html">]<A HREF="http://www.wwpdb.org/documentation/file-format">PDB format</A>[{{or XML format}}]. A separate section of this document provides <A HREF="#MmdbsrvSave">additional details about structure data download options</A> and what data are saved in each case</A>.[<A HREF="#MmdbsrvSave"><span style="color:#d70000">illustration</span></A>]</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR -->
|
||
|
||
<!-- ========= END_OLD:DISPLAY_OPTIONS_STRUCTURE_VIEW_DISPLAY_AS_MENU ========== -->
|
||
|
||
<!-- ======== DOWNLOAD_STRUCTURE_DATA_OPTIONS: FILE_FORMAT ======== -->
|
||
<!-- ======= WAS:DISPLAY_OPTIONS_STRUCTURE_DRAWING_COMPLEXITY_MENU ======== -->
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"><A NAME="MmdbsrvStructureViewDataSet"></A><A NAME="MmdbsrvStructureViewComplexity"></A><A NAME="MmdbsrvStructureViewDrawing"></A><B>Data Set</B></TD>
|
||
<TD valign="top" align="left" colspan="2">The <B>"Data Set" options</B> that you select in the "Download Structure Data" box of an <A HREF="#SummaryPage">MMDB summary page</A> will <B>act upon the</B> <A HREF="#MmdbsrvDisplayOptions">biological unit(s) or asymmetric unit currently displayed</A> in your browser window, and allow you to download the data file in varying levels of detail (complexity). <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewDataSetAllAtoms"></A><A NAME="MmdbsrvStructureViewComplexityAllAtoms"></A><A NAME="MmdbsrvStructureViewDrawingAllAtoms"></A><LI><B>Single 3D Structure</B></LI></TD>
|
||
<TD valign="top" align="left">Displays the detailed model, showing the coordinates of each atom in the structure. This option, which is the default, transmits a large amount of structure data and it may therefore take some time to load the structures.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewDataSetAllModels"></A><A NAME="MmdbsrvStructureViewComplexityAllModels"></A><A NAME="MmdbsrvStructureViewDrawingAllModels"></A><LI><B>All 3D Structures</B></LI></TD>
|
||
<TD valign="top" align="left">This option is available only when the Cn3D file format is selected. It displays all members of <A HREF="#DataTypeExperimentalMethods">NMR</A> ensembles or correlated disorder sets from crystallography. You can also see movie-like animations of multiple models with Cn3D.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewDataSetBackbone"></A><A NAME="MmdbsrvStructureViewComplexityBackbone"></A><A NAME="MmdbsrvStructureViewDrawingBackbone"></A><A NAME="MmdbsrvStructureViewDrawingAlphaCarbons"></A><LI><B>Alpha Carbons</B></LI></TD>
|
||
<TD valign="top" align="left">Displays only alpha-carbon (protein) or phosphate (DNA) coordinates for simple representation of protein or nucleic acid backbones, respectively. This option transmits only a subset of the data points from a structure record and therefore loads relatively quickly. This option is selected by default for structures with >25,000 atoms. If you are viewing the structure summary page for an <A HREF="#DataTypeExperimentalMethods">NMR</A> ensemble or a correlated disorder set from crystallography, this option will download backbone data only for the first model in the set.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="120" valign="top" align="left"> </TD>
|
||
<TD width="150" valign="top" align="left"><A NAME="MmdbsrvStructureViewDataSetPDBdataset"></A><A NAME="PDBdataset"></A><A NAME="DownloadPDB"></A><A NAME="DownloadPDBFile"></A><A NAME="DownloadSourcePDBFile"></A><A NAME="DownloadPDBSourceFile"></A><A NAME="PDBSourceFile"></A><LI><B>PDB source file</B><!-- B>PDB data set</B --></LI></TD>
|
||
<TD valign="top" align="left">The "Download" button beside the PDB ID (in the upper right corner of a <A HREF="#SummaryPage">structure summary page</A>) downloads the original <A HREF="#SourceDatabases">PDB source file</A> from which the MMDB record was derived. That file contains data for the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> of the structure.<BR><BR>
|
||
<I>Note that the "<A HREF="#MmdbsrvStructureView">Download Structure Data</A>" section of a structure summary page also provides a "PDB" option in the "Format" pulldown menu. That option does not save a copy of the PDB source file, but instead saves copy of the structure record, in <A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A>, after it has undergone <A HREF="#DataProcessing">MMDB data processing</A>.
|
||
The differences are explained in a separate section of this document on "<A HREF="#MmdbsrvSave">additional details about structure data download options</A> > <A HREF="#MmdbsrvSavePDBformat">PDB format</A> > <A HREF="#MmdbsrvSavePDBformatDetails">details about the data that are saved</A>."
|
||
<!-- A separate section of this document provides <A HREF="#MmdbsrvSave">additional details about structure data download options</A> and the <A HREF="#MmdbsrvSavePDBformat">details about the data that are saved when the option for PDB format is selected</A>.) --></I></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
<!-- TD valign="top" align="left">This option is available only when the viewing/saving the <A HREF="#DataProcessingAsymmetricUnit">asymmetric unit</A> in PDB format and saves an exact copy of the original PDB source file.<BR>
|
||
(A separate section of this document provides <A HREF="#MmdbsrvSave">additional information</A> > <A HREF="#MmdbsrvSavePDBformat">PDB format</A> > <A HREF="#MmdbsrvSavePDBformatDetails"><B>details about the data that are saved</B></A> if an option <B>other than</B> "PDB data set" is chosen.)</TD>
|
||
<TD valign="top" width="10"> </TD -->
|
||
</TR>
|
||
|
||
|
||
<!-- ======== END_DOWNLOAD_STRUCTURE_DATA_OPTIONS: FILE_FORMAT ======== -->
|
||
<!-- ======= END_WAS:DISPLAY_OPTIONS_STRUCTURE_DRAWING_COMPLEXITY_MENU ======== -->
|
||
|
||
<!-- ========= OLD:DISPLAY_OPTIONS_VIEW_STRUCTURE_BUTTON ========== -->
|
||
|
||
<!-- TR>
|
||
<TD width="120" valign="top" align="left"><A NAME="MmdbsrvStructureViewButton"></A><B>"View Structure" button</B></TD>
|
||
<TD valign="top" align="left" colspan="2">The "View Structure" button with either (a) open an interactive 3D display of the structure, (b) open the data file in the browser window, or (c) save the data file to your computer, depending upon which option you have selected from the <A HREF="#MmdbsrvStructureViewTasks">Tasks</A> menu. If you have selected "Display Structure" from that menu, note that the <A HREF="#MmdbsrvStructureViewProgram">Program</A> you have chosen must already be installed on your computer as a helper application in order for the "View Structure" button to work. The program does not need to be installed if you just want to view the underlying data file as text or save it to a file.</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="4" valign="top" class="MiniText"> </TD>
|
||
</TR -->
|
||
|
||
<!-- ======= END_OLD:DISPLAY_OPTIONS_VIEW_STRUCTURE_BUTTON ======== -->
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ===== END_DOWNLOAD_STRUCTURE_DATA_OPTIONS: FILE_FORMAT_and_DATASET ==== -->
|
||
|
||
<!-- ===== DAGGER_CROSS_REFERENCE_TO_SAVE_STRUCTURE_RECORD_EXAMPLES ====== -->
|
||
|
||
<A NAME="NoteSaveRecord"></A>
|
||
|
||
<!-- BLOCKQUOTE>
|
||
|
||
<B>†</B> The "<A HREF="#MmdbsrvSave"><B>Save structure record</B></A>" section of this document provides specific examples of the display option combinations to use in order to save the file in <A HREF="#MmdbsrvSaveASN1format"><B>ASN.1 format</B></A> or <A HREF="#MmdbsrvSavePDBformat"><B>PDB format</B></A>.
|
||
|
||
</BLOCKQUOTE -->
|
||
|
||
|
||
<!-- === ADDITIONAL_DETAILS_ABOUT_MMDBSRV_SAVE_STRUCTURE_RECORD === -->
|
||
<!-- ============ WAS: MMDBSRV_SAVE_STRUCTURE_RECORD ============== -->
|
||
|
||
<A NAME="MmdbsrvSave"></A>
|
||
<A NAME="SaveStructure"></A>
|
||
<A NAME="Save"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" align="left" class="NormalText"><B>Additional details about structure data download options</B> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<!-- MINI_TOC FOR ADDITIONAL_DETAILS_ABOUT_MMDBSRV_SAVE_STRUCTURE_RECORD -->
|
||
|
||
<TR>
|
||
<TD valign="top" class="NormalText">
|
||
<BLOCKQUOTE>
|
||
<A HREF="#DownloadStructureDataIllustration">annotated illustration of download options</A> |<BR>
|
||
<A HREF="#MmdbsrvSaveDataFile">details about data saved in each file format:</A> <A HREF="#MmdbsrvSaveASN1format">ASN.1 (Cn3D)</A>, <A HREF="#MmdbsrvSavePDBformat">PDB</A>, <A HREF="#MmdbsrvSaveXMLformat">XML and JSON</A>, <A HREF="#MmdbsrvSavePNGformat">PNG (image)</A> |<BR><A HREF="#MmdbsrvSave3dView">save image of 3D structure</A> | <A HREF="#MmdbsrvSaveComponents">save structure components</A>
|
||
</BLOCKQUOTE>
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<!-- END_MINI_TOC FOR ADDITIONAL_DETAILS_ABOUT_MMDBSRV_SAVE_STRUCTURE_RECORD -->
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ===== TABLE_OF_DOWNLOAD_STRUCTURE_DATA_MENU_OPTIONS ==== -->
|
||
|
||
<!-- BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top">The "<A HREF="#MmdbsrvStructureView"><B>Download Structure Data</B></A>" section of a <A HREF="#SummaryPage">structure summary</A> page enables you to <B>save the data file</B> for a structure record. An annotated illustration of download options is below, followed by <A HREF="#MmdbsrvSaveDataFile">details about data saved</A> in the following file formats: <A HREF="#MmdbsrvSaveASN1format"><B>ASN.1 (Cn3D)</B></A>, <A HREF="#MmdbsrvSavePDBformat"><B>PDB</B></A>, <A HREF="#MmdbsrvSaveXMLformat"><B>XML and JSON</B></A>. There are also various methods to <A HREF="#MmdbsrvSave3dView">save an <B>image</B> of the 3D structure</A>, and to <A HREF="#MmdbsrvSaveComponents">save the structure's <B>molecular components</B></A>.</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="MiniText"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE -->
|
||
|
||
<!-- ========== MMDBSRV_DOWNLOAD_STRUCTURE_DATA_ILLUSTRATION =========== -->
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" align="left" width="570"><A NAME="DownloadStructureDataIllustration"></A><A NAME="MmdbsrvSaveIllustration"></A><A NAME="SaveStructureIllustration"></A>
|
||
<B>Annotated illustration of download options</B> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A><BR><BR>
|
||
<IMG src="images/1PTH_structure_save_options.png" height="705" width="800" border="0" align="left" valign="center" alt="Illustration showing how to save a structure record in ASN.1 format or PDB format by selecting the desired options from the Program, Tasks, and Complexity menus in the See in 3D/Save box on a structure summary page."><BR></TD>
|
||
<TD valign="TOP" align="Left">
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="top" class="NormalText"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ======== END_MMDBSRV_DOWNLOAD_STRUCTURE_DATA_ILLUSTRATION ========= -->
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD colspan="3" valign="top" class="NormalText"><A NAME="MmdbsrvSaveDataFile"></A><B>Details about the data that are saved in each of the following file formats</B>: <A HREF="#MmdbsrvSaveASN1format">ASN.1 (Cn3D)</A>, <A HREF="#MmdbsrvSavePDBformat">PDB</A>, <A HREF="#MmdbsrvSaveXMLformat">XML and JSON</A> <img SRC="../../IMG/spacer.gif" width="10" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A><BR><BR></TD>
|
||
</TR>
|
||
|
||
|
||
<TR>
|
||
<TD width="30" valign="TOP" class="NormalText"> </TD>
|
||
<TD valign="TOP"><A NAME="MmdbsrvSaveCn3Dformat"></A><A NAME="MmdbsrvSaveASN1format"></A><B>ASN.1 Format:</B>  To save the structure's data file in <A HREF="../../asn1.html"><B>ASN.1 format</B></A>, an International Standards Organization (ISO) data format that is viewable in the free <A HREF="/Structure/CN3D/cn3d.shtml"><B>Cn3D</B></A> program, select the following combination of options (on the web interface, or through the <A HREF="#MmdbsrvStructureViewURLformat">Web API</A>):<BR>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormat">File Format</A> : <A HREF="#MmdbsrvStructureViewFileFormatCn3D">ASN.1 (Cn3D)</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSet">Data Set</A> : your choice of <A HREF="#MmdbsrvStructureViewDataSetAllAtoms">Single 3D Structure</A>, <A HREF="#MmdbsrvStructureViewDataSetAllModels">All 3D Structures</A>, or <A HREF="#MmdbsrvStructureViewDataSetBackbone">Alpha Carbons</A>.</LI>
|
||
<LI>Press the "Download" button.</LI>
|
||
</UL>
|
||
<P class="indent20">
|
||
<B><A NAME="MmdbsrvSaveCn3DformatDetails"></A>Details about the data that are saved</B>:<BR>
|
||
(1) For X-ray crystallography or neutron diffraction of crystal structures: (a) If you have chosen to <A HREF="#MmdbsrvDisplayOptions">display</A> the <!-- {{"unique biological units"}} --> "first <A HREF="#DataProcessingBiologicalForms">biological unit</A>" or "all biological units" on the structure summary page, the "Download" operation will save the data for the specific biological unit displayed in the molecular graphic. The saved file will include sequence and spatial coordinate data that were present in the original <A HREF="#SourceDatabases">PDB source file</A> as well as data that were generated at NCBI by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>, if applicable to that biological unit. (b) If you have selected the "<A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>" <A HREF="#MmdbsrvDisplayOptions">display</A> option, the "Download" operation will save the data that were present in the PDB source file, whether those data represented all, part, or multiple copies of a biological unit. The saved file will not include any data generated at NCBI by applying transformations from crystallographic symmetry.<BR>
|
||
(2) For structures resolved by <A HREF="#DataTypeExperimentalMethods">experimental methods</A> other than X-ray crystallography or neutron diffraction of crystal structures, the "Download" operation will save the data that were provided by the author in the PDB source file. The concepts of asymmetric unit, biological units, and crystallographic symmetry do not apply to these structures.<BR>
|
||
Note for both (1) and (2) above: The saved file may also include some modifications (relative to the original PDB source file) that occurred as a standard part of MMDB data processing. Some examples are provided below in the notes about PDB format.
|
||
</P><BR>
|
||
</TD>
|
||
<TD width="30" valign="TOP" class="NormalText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="30" valign="TOP" class="NormalText"> </TD>
|
||
<TD valign="TOP"><A NAME="MmdbsrvSavePDBformat"></A><B>PDB Format:</B>  To save the structure's data file in <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format"><B>PDB format</B></A>, which is viewable in <A HREF="http://www.umass.edu/microbio/rasmol/"><B>Rasmol</B></A> or other programs that accept PDB format, select the following combination of options (on the web interface, or through the <A HREF="#MmdbsrvStructureViewURLformat">Web API</A>):<BR>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormat">File Format</A> : <A HREF="#MmdbsrvStructureViewFileFormatPDB">PDB</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSet">Data Set</A> : your choice of <A HREF="#MmdbsrvStructureViewDataSetAllAtoms">Single 3D Structure</A> <!-- A HREF="#MmdbsrvStructureViewDataSetAllModels">All 3D Structures</A --> or <A HREF="#MmdbsrvStructureViewDataSetBackbone">Alpha Carbons</A><!-- You can also download the original <A HREF="#MmdbsrvStructureViewDataSetPDBdataset">PDB source file</A>, if desired --></LI>
|
||
<!-- LI><I>(<A HREF="#MmdbsrvStructureViewComplexity">Complexity</A> options (<A HREF="#MmdbsrvStructureViewComplexityAllAtoms">All Atoms</A>, <A HREF="#MmdbsrvStructureViewComplexityBackbone">Backbone</A>, or <A HREF="#MmdbsrvStructureViewComplexityAllModels">All Models</A>) are not available for the "Rasmol" program option. They are only available for Cn3D.)</I></LI -->
|
||
<LI>Press the "Download" button.</LI>
|
||
</UL>
|
||
<P class="indent20"><A NAME="MmdbsrvSavePDBformatDetails"></A><B>Details about the data that are saved</B>: The PDB-formatted file that is downloaded when you select "Format: PDB" (in the "<A HREF="#MmdbsrvStructureView">Download Structure Data</A>" section of a structure summary page) has undergone content validation that is a standard part of <A HREF="#DataProcessing">data processing</A>. Its content may therefore be somewhat different from that of the original PDB record. For example, some PDB records may have discontinous residue numbers, which exist in a free text field. MMDB assigns a consecutive series of positive integers to residues in biopolymers, using a numerical data field. In addition, MMDB resolves some discrepancies that might exist between the SEQRES records and the atomic coordinates. For example, if the structure's atomic coordinates reveal the presence of amino acids or nucleotides that are not listed in the SEQRES records of an original PDB file, MMDB will derive the biopolymer sequence from the atomic coordinates and not from the original SEQRES records. The derived biopolymer sequence will then appear in the MMDB record, and in the SEQRES records of the PDB-formatted file saved from the MMDB database. As a third example, the spans of <!-- A HREF="#FourLevelsOfStructure" --><A HREF="#DataProcessingSecondaryStructures">secondary structures</A> annotated on proteins might vary between PDB and MMDB records, as NCBI algorithmically identifies alpha helices and beta strands using purely geometric criteria and annotates the proteins using that information rather than the spans indicated in the original PDB file. Therefore, the content of a PDB-formatted record you save from an MMDB <A HREF="#SummaryPage">structure summary page</A> may be different from the content of the original PDB file.<!-- {{Any other notes to include about the content of the MMDB-generated PDB files, such as interaction data or merged PDB split files?}} --><BR><BR>
|
||
To save an exact copy of the original <A HREF="#SourceDatabases">PDB source file</A>, click on the "Download" button that appears next to the PDB ID in the upper right hand corner of a <A HREF="#SummaryPage">structure summary page</A>.
|
||
<!-- To save an exact copy of the original <A HREF="#SourceDatabases"><B>PDB source file</B></A>, <A HREF="#MmdbsrvDisplayOptions"><B>display</B></A> the <B>asymmetric unit</B> and select "<A HREF="#MmdbsrvStructureViewFileFormat"><B>File Format</B></A>: <B>PDB</B>" + "<A HREF="#MmdbsrvStructureViewDataSet"><B>Data Set</B></A>: <B>PDB data set</B>." -->
|
||
</P><BR>
|
||
</TD>
|
||
<TD width="30" valign="TOP" class="NormalText"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="30" valign="TOP" class="NormalText"> </TD>
|
||
<TD valign="TOP"><A NAME="MmdbsrvSaveXMLformat"></A><A NAME="MmdbsrvSaveJSONformat"></A><B>XML and JSON Formats:</B>  To save the structure's data file in <A HREF="/IEB/ToolBox/XML/ncbixml.txt">XML</A> or <A HREF="http://json.org/">JSON</A> formats, select the following combination of options (on the web interface, or through the <A HREF="#MmdbsrvStructureViewURLformat">Web API</A>):<BR>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvStructureViewFileFormat">File Format</A> : <A HREF="#MmdbsrvStructureViewFileFormatXML">XML</A> or <A HREF="#MmdbsrvStructureViewFileFormatJSON">JSON</A></LI>
|
||
<LI><A HREF="#MmdbsrvStructureViewDataSet">Data Set</A> : your choice of <A HREF="#MmdbsrvStructureViewDataSetAllAtoms">Single 3D Structure</A>, <A HREF="#MmdbsrvStructureViewDataSetAllModels">All 3D Structures</A>, or <A HREF="#MmdbsrvStructureViewDataSetBackbone">Alpha Carbons</A>.</LI>
|
||
<LI>Press the "Download" button.</LI>
|
||
</UL>
|
||
<P class="indent20">
|
||
<B><A NAME="MmdbsrvSaveCn3DformatDetails"></A>Details about the data that are saved</B>:<BR>
|
||
The "Download Structure Data" function on an <A HREF="#SummaryPage">MMDB summary page</A> will <B>act upon the</B> <A HREF="#MmdbsrvDisplayOptions">biological unit(s) or asymmetric unit currently displayed</A> in your browser window, and allow you to download the data file in varying levels of detail (also referred to as varying levels of complexity, or <A HREF="#MmdbsrvStructureViewDataSet">data sets</A>). It is also possible to save the data by using the <A HREF="#WebAPI">Web API</A><!-- A HREF="#MmdbsrvStructureViewURLformat">specially formatted URL</A -->.
|
||
</P><BR>
|
||
</TD>
|
||
<TD width="30" valign="TOP" class="NormalText"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ===== END_TABLE_OF_DOWNLOAD_STRUCTURE_DATA_MENU_OPTIONS ==== -->
|
||
|
||
<!-- ============= MMDBSRV_SAVE_IMAGE_OF_3D_STRUCTURE ============== -->
|
||
|
||
<A NAME="MmdbsrvSave3dView"></A>
|
||
<A NAME="MmdbsrvSavePNGformat"></A>
|
||
<A NAME="MmdbsrvSavePNGimage"></A>
|
||
<A NAME="MmdbsrvSaveImage"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" align="left" class="NormalText"><B>Save image of 3D structure</B> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="TOP">
|
||
|
||
<P class="indent30">It is possible to <B>save an image of the 3D structure</B> in a number of ways, with varying degrees of customization possible:<BR></P>
|
||
|
||
<UL>
|
||
|
||
<LI>To save the <B>default image of a 3D structure</B>:</LI><BR>
|
||
<UL>
|
||
<LI>Open the <A HREF="#SummaryPage">summary page</A> page for the desired structure and view its <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A></LI>
|
||
<LI>Use the <A HREF="#MmdbsrvStructureView">Download Structure Data</A> box that appears beside the <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A>, and select the options for <SPAN style="background-color: #FFFF00"><A HREF="#MmdbsrvStructureViewFileFormat">Format</A>: <A HREF="#MmdbsrvStructureViewFileFormatPNG"><B>PNG (image)</B></A></SPAN></LI>
|
||
<LI>Click on the "<B>Download</B>" button</LI>
|
||
</UL><BR>
|
||
|
||
<LI>To <B>customize the viewing angle</B> and/or background color, apply termini labels, or view solvent accessible surface, and then <B>save the resulting snapshot</B>:</LI><BR>
|
||
<UL>
|
||
<LI>Open the <A HREF="#SummaryPage">MMDB summary page</A> page for the desired structure and view its <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A>, which by default shows a static image.</LI>
|
||
<LI>Click the <B>"3D view" button</B> <IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_button_3d_view.png" width="57" height="19" border="0"> in the lower left corner of the static image to <B>load an interactive view</B> of the structure. (The interactive view uses a <SPAN style="background-color: #FFFF00"><B>simple version of </B> <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A></SPAN>, NCBI's web-based 3D structure viewer, and requires a web browser that supports <a href="https://get.webgl.org/">WebGL</a>.)</LI>
|
||
<LI>Once the structure spins to the desired position, <B>click on the structure to stop the spin</B></LI>
|
||
<LI><B>Right click</B> to open a <B>menu</B> that allows you to control various aspects of the display and/or to "export image."</LI>
|
||
<LI>Select "<B>Export Image</B>" to open the view in a separate window.</LI>
|
||
<LI>Right click on the exported image to use the browser's "<B>save image as</B>" function.</LI>
|
||
<LI><B>Reload</B> the page to reveal the "3D view" button again, then <B>repeat</B> the process as many times as desired in order to save snapshots of the structure at the desired angles.</LI>
|
||
<LI>Each time you select "Export Image," a separate window will open, making it possible to <B>view the structure from many angles simultaneously</B>.</LI>
|
||
</UL><BR>
|
||
|
||
<LI>To <B>customize rendering style</B> of the structure, <B>highlight selected regions</B> of the structure and/or corresponding <B>sequence data</B>, add <B>labels</B>, etc., and then <B>save the state</B> of the structure so you can reload it in the <SPAN style="background-color: #FFFF00"><B>full-featured version of </B> <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A></SPAN> in the future:</LI><BR>
|
||
|
||
<UL>
|
||
<LI>Open the <A HREF="#SummaryPage">MMDB summary page</A> page for the desired structure and view its <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A>, which by default shows a static image.</LI>
|
||
<LI>Click the <B>"3D view" button</B> <!-- IMG SRC="images" width="44" height="38" border="0" --><IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_button_3d_view.png" width="57" height="19" border="0"> in the lower left corner of the static image to <B>load an interactive view</B> of the structure. (The interactive view uses a <SPAN style="background-color: #FFFF00"><B>simple version of </B> <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A></SPAN>, NCBI's web-based 3D structure viewer, and requires a web browser that supports <a href="https://get.webgl.org/">WebGL</a>.)</LI>
|
||
<LI>Then click the "full-featured 3D viewer" button <IMG SRC="images/mmdbsrv_molecular_graphic_icn3d_control_button_full_featured_3d_viewer.png" WIDTH="150" HEIGHT="19" BORDER="0" ALT="button that launches full featured iCn3D in another window"> to launch the <SPAN style="background-color: #FFFF00"><b>full version of </b><A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A></SPAN> in another window.</LI>
|
||
<LI>Use the various menu options to render the structure with the desired style, color, labels, viewing angle, etc.</LI>
|
||
<LI>Select the <B>File/Save Files/State File</B> to save the state of the structure in a file. (The file will be named "NXXX_statefile" by default, unless you select the "Save As" option in your browser, and file will be in <B>*.txt format</B>. The NXXX in the default filename represents the PDB ID of the structure.) You can then later open the statefile through the iCn3D "File/Open State" menu option.</LI>
|
||
<LI>Alternatively, you can select the <B>File/Save Files/iCn3D PNG Image</B> to save both the customized 3D image (as a <B>*.png file</B>) and the state of the structure (as an <B>*.html file</B>).</LI>
|
||
<UL>
|
||
<LI>Specifically, the "File/Save Files/iCn3D PNG Image" option saves two files with a single action. The first file will be named NXXX_xxxxxxxxxxxxxxxxx.png, and the second will be named NXXX_xxxxxxxxxxxxxxxxx.html, where NXXX in the default filename represents the PDB ID of the structure and xxxxxxxxxxxxxxxxx is a hash tag that represents the customizations you made to the view. (Example filenames are: "1TUP-pgmMZ96uF2YhEsNc6.png" and "1TUP-pgmMZ96uF2YhEsNc6.html").</LI>
|
||
<LI>Additionally, the <B>*.png file</B> includes a "<a href="../../icn3d/docs/icn3d_help.html#FileShareLink">share URL</a>" at the bottom. If a user opens that file in iCn3D, they will be able to see the structure in the same state in which they saved it, and it will be a live structure, so they can continue to view it interactively in iCn3D.</LI>
|
||
</UL>
|
||
</UL><BR>
|
||
|
||
<LI>To <B>render and save images using the wide range of controls</B> that are available in <SPAN style="background-color: #FFFF00"><B>NCBI's free standalone</B> <a href="../../CN3D/cn3d.shtml"><B>Cn3D</B></a></SPAN> structure-viewing program:</LI><BR>
|
||
|
||
<UL>
|
||
<LI>Open the <A HREF="#SummaryPage">MMDB summary page</A> for the structure of interest.</LI>
|
||
<LI>In the "<A HREF="#MmdbsrvStructureView">Download Structure Data</A>" box, select "<A HREF="#MmdbsrvStructureViewFileFormat">Format</A>:<A HREF="#MmdbsrvStructureViewFileFormatCn3D">ASN.1 (Cn3D)</A>" and the desired "<A HREF="#MmdbsrvStructureViewDataSet">Data Set</A>," then press the "<B>Download</B>" button.</LI>
|
||
<LI>Open the file in Cn3D, where you can render, label, color the structure as desired. (To do this, <a HREF="../../CN3D/cn3dinstall.shtml">install</a> Cn3D on your computer, and if desired, <A HREF="../../CN3D/cn3dinstall.shtml#browser">configure</A> it as a helper app.)</LI>
|
||
<LI>The <A HREF="/Structure/CN3D/cn3dtut.shtml">Cn3D tutorial</A>, provides detailed instructions on <A HREF="/Structure/CN3D/cn3dtutP6.shtml#output">saving structures and images</A>, including any special <A HREF="/Structure/CN3D/cn3dtutP6.shtml">annotations</A> you have made to the 3D structure view, such as adding labels or using specific drawing styles.</LI>
|
||
</UL><BR>
|
||
|
||
<LI>To <B>render and save images using the controls</B> provided by <B>external 3D structure viewing programs</B> that read <!-- A HREF="http://www.wwpdb.org/documentation/file-format" --><A HREF="#MmdbsrvStructureViewFileFormatPDB">PDB file format</A>, such as <A HREF="http://www.umass.edu/microbio/rasmol/">Rasmol</A>:</LI><BR>
|
||
|
||
<UL>
|
||
<LI>Open the <A HREF="#SummaryPage">MMDB summary page</A> for the structure of interest.</LI>
|
||
<LI>In the "<A HREF="#MmdbsrvStructureView">Download Structure Data</A>" box, select "<A HREF="#MmdbsrvStructureViewFileFormat">Format</A>:<A HREF="#MmdbsrvStructureViewFileFormatPDB">PDB</A>" and the desired "<A HREF="#MmdbsrvStructureViewDataSet">Data Set</A>," then press the "<B>Download</B>" button.</LI>
|
||
<LI>Open the file in any 3D structure viewer (e.g., <A HREF="http://www.umass.edu/microbio/rasmol/">Rasmol</A>) that reads PDB file format.</LI>
|
||
<LI>Render, label, color, and save the structure as desired, according to the instructions provided by the structure viewing program's help documentation</LI>
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============= MMDBSRV_SAVE_COMPONENTS ============== -->
|
||
|
||
<A NAME="MmdbsrvSaveComponents"></A>
|
||
|
||
<!-- P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Save structure components</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P -->
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="2" class="TableText1">
|
||
|
||
<TR>
|
||
<TD valign="top" align="left" class="NormalText"><B>Save structure components</B> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD valign="TOP">
|
||
|
||
<BLOCKQUOTE>
|
||
<!-- B>Save components provided by source database plus additional records associated with the biosystem via NCBI data processing:</B><BR><BR -->
|
||
|
||
The sequence and/or chemical records for the <A HREF="#MmdbsrvMolecularComponents">molecular components</A> of a structure can be retrieved by: (a) following the link for each component displayed in the tabular summary at the bottom of a <A HREF="#SummaryPage">structure record</A> to its corresponding record in the Entrez Protein, Nucleotide, and/or PubChem database, or (b) selecting the appropriate items from the "<A HREF="#DocSumLinks">Links</A>" pop-up menus on the <A HREF="#SearchResults">search results (docsum)</A> page for the structure.<BR><BR>
|
||
|
||
Once you are viewing the components in the relevant Entrez database, you can display and/or save those records in any format that is available for that database. For example, records from the <A HREF="/protein">Entrez Protein</A> database can be saved in <a href="https://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml">FASTA</a> format (which is convenient for sequence analysis), as a list of <A HREF="/Sitemap/samplerecord.html#GIpB">GI numbers</A>, or in other formats such as GenPept (which contains sequence data plus annotations, similar to <a HREF="/Sitemap/samplerecord.html">GenBank</a> format). <I>The <A HREF="/books/NBK3837/#EntrezHelp.Displaying_and_Saving_a_Set_o">Entrez help document</A> provides additional information about sequence database record formats. The <A HREF="/books/NBK3841/#EntrezGene.How_Data_Are_Displayed_Displa">Entrez Gene help</A> and <A HREF="https://pubchem.ncbi.nlm.nih.gov/help.html#PubChem_Summary">PubChem help</A> documents describe record formats for genes and small molecules,</I> respectively.<BR><BR>
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
<TD valign="top" width="10"> </TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ======= MMDBSRV_MOLECULES_AND_INTERACTIONS_GRAPHIC_SUMMARY ========== -->
|
||
|
||
<A NAME="MolecularComponents"></A>
|
||
<A NAME="MmdbsrvMolecularComponents"></A>
|
||
<A NAME="MmdbsrvGraphicSummary"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Molecular Components</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
||
</P>
|
||
|
||
<!-- ============ MINI_TOC FOR MOLECULES_AND_INTERACTIONS ============== -->
|
||
|
||
<BLOCKQUOTE>
|
||
<UL>
|
||
<LI><A HREF="#MolecularComponentsTable"><!-- A HREF="#MmdbsrvMolecularComponentsTable" -->Tabular list of molecular components</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvColumnHeaders">Column headers: label, count, molecule</A></LI>
|
||
<!-- UL>
|
||
<LI><A HREF="#MmdbsrvColumnHeadersLabel">Label</A></LI>
|
||
<LI><A HREF="#MmdbsrvColumnHeadersCount">Count</A></LI>
|
||
<LI><A HREF="#MmdbsrvColumnHeadersMolecule">Molecule</A></LI>
|
||
<LI><A HREF="#MmdbsrvColumnHeadersInteractions">Interactions</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
<LI><A HREF="#MmdbsrvProteins">Proteins</A></LI>
|
||
<UL>
|
||
<LI>
|
||
<A HREF="#MmdbsrvProteins">Molecule label, count, & name</A>
|
||
<!-- A HREF="#MmdbsrvProteinsMoleculeLabel">label</A -->
|
||
<!-- A HREF="#MmdbsrvProteinsMoleculeCount">count</A -->
|
||
<!-- A HREF="#MmdbsrvProteinsMoleculeName">name</A -->
|
||
<!-- A HREF="#MmdbsrvProteinsMoleculeInteractions">interactions</A -->
|
||
</LI>
|
||
<LI><A HREF="#MmdbsrvProteinsGeneSymbol">Gene symbol</A></LI>
|
||
<LI><A HREF="#MmdbsrvProteinsShowAnnotation">Protein annotation graphic</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvProteins3dDomains">3D domains</A></LI>
|
||
<LI><A HREF="#MmdbsrvProteinsClassification">Domain families (protein classification)</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#MmdbsrvProteinsClassificationSpecificHits">Specific hits</A></LI>
|
||
<LI><A HREF="#MmdbsrvProteinsClassificationSuperfamilies">Superfamilies</A></LI>
|
||
<LI><A HREF="#MmdbsrvProteinsClassificationMultidomains">Multidomains</A></LI>
|
||
</UL>
|
||
<!-- LI><A HREF="#MmdbsrvProteinsSimilarSequences">Similar Sequences (BLAST)</A></LI -->
|
||
<!-- LI><A HREF="#MmdbsrvProteinsSimilarStructures">Similar 3D Structures: VAST</A></LI -->
|
||
</UL>
|
||
<!-- LI><A HREF="#MmdbsrvProteinsMoleculeInteractions">Interactions</A></LI -->
|
||
</UL>
|
||
<LI><A HREF="#MmdbsrvNucleotides">Nucleotides</A></LI>
|
||
<UL>
|
||
<LI>
|
||
<A HREF="#MmdbsrvNucleotidesMoleculeName">Molecule label, count, & name</A>
|
||
<!-- A HREF="#MmdbsrvNucleotidesMoleculeLabel">label</A -->
|
||
<!-- A HREF="#MmdbsrvNucleotidesMoleculeCount">count</A -->
|
||
<!-- A HREF="#MmdbsrvNucleotidesMoleculeName">name</A -->
|
||
<!-- A HREF="#MmdbsrvNucleotidesMoleculeInteractions">interactions</A -->
|
||
</LI>
|
||
<LI><A HREF="#MmdbsrvNucleotidesThumbnail">Thumbnail graphic</A></LI>
|
||
<!-- LI><A HREF="#MmdbsrvNucleotidesMoleculeInteractions">Interactions</A></LI -->
|
||
</UL>
|
||
<LI><A HREF="#MmdbsrvChemicals">Chemicals</A></LI>
|
||
<UL>
|
||
<LI>
|
||
<A HREF="#MmdbsrvChemicalsMoleculeName">Molecule label, count, & name</A>
|
||
<!-- A HREF="#MmdbsrvChemicalsMoleculeLabel">label</A -->
|
||
<!-- A HREF="#MmdbsrvChemicalsMoleculeCount">count</A -->
|
||
<!-- A HREF="#MmdbsrvChemicalsMoleculeName">name</A -->
|
||
<!-- A HREF="#MmdbsrvChemicalsMoleculeInteractions">interactions</A -->
|
||
</LI>
|
||
<LI><A HREF="#MmdbsrvChemicalsThumbnail">Thumbnail graphic</A></LI>
|
||
<!-- LI><A HREF="#MmdbsrvChemicalsMoleculeInteractions">Interactions</A></LI -->
|
||
</UL>
|
||
<LI><A HREF="#MmdbsrvNonStandardBiopolymers">Non-standard biopolymers</A></LI>
|
||
<UL>
|
||
<LI>
|
||
<A HREF="#MmdbsrvNonStandardBiopolymersMoleculeName">Molecule label, count, & name</A>
|
||
<!-- A HREF="#MmdbsrvNonStandardBiopolymersMoleculeLabel">label</A -->
|
||
<!-- A HREF="#MmdbsrvNonStandardBiopolymersMoleculeCount">count</A -->
|
||
<!-- A HREF="#MmdbsrvNonStandardBiopolymersMoleculeName">name</A -->
|
||
<!-- A HREF="#MmdbsrvNonStandardBiopolymersMoleculeInteractions">interactions</A -->
|
||
</LI>
|
||
<!-- LI><A HREF="#MmdbsrvNonStandardBiopolymersMoleculeThumbnail">Thumbnail graphic</A></LI -->
|
||
<!-- LI><A HREF="#MmdbsrvNonStandardBiopolymersMoleculeInteractions">Interactions</A></LI -->
|
||
</UL>
|
||
|
||
<!-- LI><A HREF="#MmdbsrvInteractions">Observed [Inferred?] Interactions</A></LI -->
|
||
<!-- UL>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
<LI><A HREF="#Mmdbsrv_______">___________</A></LI>
|
||
</UL -->
|
||
</UL>
|
||
</BLOCKQUOTE>
|
||
<br>
|
||
|
||
<!-- ============ END_MINI_TOC FOR MOLECULES_AND_INTERACTIONS ============== -->
|
||
|
||
<A NAME="MolecularComponentsTable"></A>
|
||
<A NAME="MmdbsrvMolecularComponentsTable"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<B>Tabular list of molecular components</B><BR><BR>
|
||
|
||
The <B>table</B> near the bottom of a <A HREF="#SummaryPage">structure summary page</A> <!-- (<A HREF="#SummaryPage"><span style="color:#d70000">illustration</span></A>) --> lists the <B>molecular components</B> of the structure, which may include <A HREF="#MmdbsrvProteins">proteins</A>, <A HREF="#MmdbsrvNucleotides">nucleotide sequences (DNA, RNA)</A>, and <A HREF="#MmdbsrvChemicals">chemicals</A>. <!-- These correspond to the molecules shown in the <A HREF="#MmdbsrvThumbnailSchematic">interaction schematic</A> and <A HREF="#MmdbsrvThumbnailMolecularGraphic">molecular graphic</A> for a given <A HREF="#DataProcessingBiologicalForms">biological unit</A>. -->The <B>graphics</B> and other links in the table open more detailed displays. For example, <B>mouse over</B> any icon in the graphic display on a live structure summary page (e.g., <!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885" --><A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1PTH">1PTH</A>) for more information about that component or feature annotation.<BR><BR>
|
||
|
||
For each molecular component, the following information is provided:
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- =========== MOLECULAR COMPONENTS TABLE COLUMN HEADERS ========== -->
|
||
|
||
<A NAME="MmdbsrvColumnHeaders"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" CLASS="format1 NormalText" CELLPADDING="3">
|
||
<TR>
|
||
<TD CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="MmdbsrvColumnHeadersLabel"></A><B>Label</B></TD>
|
||
<TD CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="MmdbsrvColumnHeadersCount"></A><B>Count</B></TD>
|
||
<TD CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="MmdbsrvColumnHeadersMolecule"></A><B>Molecule</B></TD>
|
||
<!-- TD CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="MmdbsrvColumnHeadersInteractions"></A><B>Interactions</B></TD -->
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD CLASS="format1A" WIDTH="34%" ALIGN="LEFT" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" CLASS="NormalText" CELLPADDING="2">
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvProteins">Proteins</A> are shown as circles</TD>
|
||
<TD WIDTH="38" ALIGN="CENTER" VALIGN="TOP"><A HREF="#MmdbsrvProteins"><IMG SRC="images/molecular_component_protein_circle.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="example of circle icons used to depict proteins"></A></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="2"><img SRC="../../IMG/spacer.gif" width="15" height="8" border="0"></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvNucleotides">Nucleotide sequences</A> are shown as squares</TD>
|
||
<TD WIDTH="38" ALIGN="CENTER" VALIGN="TOP"><A HREF="#MmdbsrvNucleotides"><IMG SRC="images/molecular_component_nucleotide_square.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="example of square icons used to depict nucleotide sequences"></A></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="2"><img SRC="../../IMG/spacer.gif" width="15" height="8" border="0"></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvChemicals">Chemicals</A> are shown as diamonds</TD>
|
||
<TD WIDTH="38" ALIGN="CENTER" VALIGN="TOP"><A HREF="#MmdbsrvChemicals"><IMG SRC="images/molecular_component_chemical_diamond.png" WIDTH="38" HEIGHT="15" BORDER="0" ALT="example of diamond shaped icons used to depict chemicals"></A></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="2"><img SRC="../../IMG/spacer.gif" width="15" height="8" border="0"></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP"><A HREF="#MmdbsrvNonStandardBiopolymers">Non-standard biopolymers</A> are shown as parallelograms</TD>
|
||
<TD WIDTH="38" ALIGN="CENTER" VALIGN="TOP"><A HREF="#MmdbsrvNonStandardBiopolymers"><IMG SRC="../../MMDB/docs/images/molecular_component_other_non_standard_biopolymers_parallelogram.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="example of parallelogram icons used to depict non-standard biopolymers"></A></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="2"><img SRC="../../IMG/spacer.gif" width="15" height="8" border="0"></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="LEFT" VALIGN="TOP" colspan="2"><I>If any protein or nucleotide molecules in the structure were generated by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>, their labels are shown as alphanumeric combinations (for example, <IMG SRC="images/molecular_component_protein_circle_crystal_symmetry.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="Example of circle icons with alphanumeric labels used to depict protein molecules generated by applying transformations from crystallographic symmetry."> or <IMG SRC="images/molecular_component_nucleotide_square_crystal_symmetry.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="Example of square icons with alphanumeric labels used to depict nucleotide sequences generated by applying transformations from crystallographic symmetry.">), indicating the source molecule from which they were generated and the copy number.
|
||
<!-- indicating the source molecule from which they were generated (to the left of the <b>underscore bar</b>) and the copy number (to the right of the underscore bar). -->Chemicals that interact only with such molecules were also generated by applying transformations from crystallographic symmetry; their labels include an underscore bar, with a number on either side of the underscore bar to indicate the source chemical and the copy number, respectively.</I></TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
<!-- If you are viewing the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A>, the icons and labels shown in the molecular components table correspond to those shown in the <A HREF="#MmdbsrvThumbnailSchematic">interaction schematic</A>.<BR><BR>
|
||
|
||
If you are viewing the structure's <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, the icons and labels reflect the set of molecules that were present in the PDB source file, which in turn can represent a complete biological unit, a portion of it, or multiple copies of it. --></TD>
|
||
|
||
<TD CLASS="format1A" WIDTH="33%" ALIGN="LEFT" VALIGN="TOP">If you are viewing the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A>, the count reflects the number of molecules that were present in the PDB source file plus any copies that were generated by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>.<BR><BR>
|
||
If you are viewing the structure's <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, the count reflects only the number of molecules that were present in the PDB source file.</TD>
|
||
|
||
<TD CLASS="format1A" WIDTH="33%" ALIGN="LEFT" VALIGN="TOP">The name or other descriptive identifier of the molecule:<BR><BR>
|
||
<!-- A HREF="#MmdbsrvProteinsMoleculeName" --><A HREF="#MmdbsrvProteins">Protein</A> names are derived from the COMPND record of the PDB source file.<BR><BR>
|
||
<!-- A HREF="#MmdbsrvNucleotidesMoleculeName" --><A HREF="#MmdbsrvNucleotides">Nucleotide sequence</A> names are derived from the COMPND record of the PDB source file<!-- (and simply show the order of nucleotides in the molecule rather than an actual molecule name) -->.<BR><BR>
|
||
<!-- A HREF="#MmdbsrvChemicalsMoleculeName" --><A HREF="#MmdbsrvChemicals">Chemical</A> names are derived from the HETNAM record of the PDB source file or from the <A HREF="/mesh">MeSH</A> terms associated with the corresponding <A HREF="https://pubchem.ncbi.nlm.nih.gov/">PubChem</A> Compound or Substance record.</TD>
|
||
|
||
<!-- TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">A list of the other molecular components within the structure with which this particular molecular component <A HREF="#DataProcessingInteractions">interacts</A> (i.e., with which it has <A HREF="#DataProcessingInteractionsContactNumberThreshold">at least 5 contacts</A> a distance of <A HREF="#DataProcessingInteractionsDistanceThreshold">4 Å or less</A> between the heavy atoms).[Å is the HTML code for Angstrom, <20>]<BR><BR>
|
||
[Follow the "<B>explore interactions</B>" link for any molecule to see <A HREF="#MmdbsrvInteractionPopup">details about its interactions</A>, or see the <A HREF="#MmdbsrvThumbnailSchematic">interactions schematic</A> for an overview of interactions among all the molecular components.<BR><BR>]
|
||
<I>If an ion is part of the structure but does not meet the contact thresholds noted above, no interactions will be listed. Such ions will also be missing from the <A HREF="#MmdbsrvThumbnailSchematic">interactions schematic</A> but they will be listed in the table of molecular components.</I><BR><BR>
|
||
<I>Interactions for short peptides, or for molecule types other than protein, DNA/RNA, and chemical, are not calculated.</I><BR><BR>
|
||
[For <A HREF="#MmdbsrvChemicals">chemicals</A>, this column says "<B>no interactions recorded</B>" [N/A (not applicable)] because interactions are listed only for biopolymers (proteins and nucleotide sequences). Therefore, if a protein or nucleotide sequence molecule interacts with a chemical (if there are at least 5 contacts a distance of 4 Å [Å is the HTML code for Angstrom, <20>] or less between the heavy atoms), the chemical will be listed in the "Interaction with" column for the corresponding biopolymer.]
|
||
</TD -->
|
||
|
||
</TR>
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- =========== END MOLECULAR COMPONENTS TABLE COLUMN HEADERS ========== -->
|
||
|
||
<!-- BLOCKQUOTE>
|
||
|
||
<Additional <B>links</B> located in the table and/or the more detailed displays retrieve <B><A HREF="#LinksSimilarStructures">similar structures</A></B> in <A HREF="/sites/entrez?db=structure">MMDB</A>, as well as <B>associated data</B> in the Entrez <A HREF="/protein/">Protein</A>, <A HREF="/nuccore/">Nucleotide</A>, and/or <A HREF="https://pubchem.ncbi.nlm.nih.gov/">PubChem</A> databases, as available for a given structure. (The <A HREF="#DocSumLinks">links pop-up menus</A> that appear on <A HREF="#SearchResults">search results</A> pages also provide access to the similar structures and associated data in other Entrez databases.)<BR><BR>
|
||
|
||
</BLOCKQUOTE -->
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="25" height="5" border="0">
|
||
|
||
<!-- =================== MOLECULAR_COMPONENTS_DETAILS ================ -->
|
||
|
||
<!-- A NAME="MmdbsrvMolecularComponents"></A -->
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="black 1px" cellpadding="4" class="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD class="format1H" colspan="2" align="left"><B>Additional details</B> for each type of component: <A HREF="#MmdbsrvProteins"><B>proteins</B></A>, <A HREF="#MmdbsrvNucleotides"><B>nucleotide sequences (DNA, RNA)</B></A>, <A HREF="#MmdbsrvChemicals"><B>chemicals</B></A>, and <A HREF="#MmdbsrvNonStandardBiopolymers"><B>non-standard biopolymers</B></A>:</TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD class="format1H" align="left"><b>Molecular Components</b></TD>
|
||
<TD class="format1H" align="center"><b>Description and Comments</b></TD>
|
||
</TR -->
|
||
|
||
<!-- =================== MOLECULAR_COMPONENTS_PROTEINS ================ -->
|
||
|
||
<TR>
|
||
<TD class="format1H" WIDTH="100" valign="top" style="white-space: nowrap;"><A NAME="MmdbsrvProteins"></A><A NAME="MmdbsrvMolecularComponentsProteins"></A><A NAME="MolecularComponentsProteins"></A><A NAME="MolecularComponentProtein"></A><B>Proteins</B></TD>
|
||
<TD class="format1B" valign="top">
|
||
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
|
||
<A NAME="MmdbsrvProteinsMoleculeLabel"></A><B>LABEL</B>: Labels for protein molecules are derived from their single letter chain codes in the <A HREF="#SourceDatabases">PDB source file</A>, and are shown as circle icons in the <A HREF="#MmdbsrvThumbnailSchematic">interaction schematic</A>, for example <IMG SRC="images/molecular_component_protein_circle.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="example of circle icons used to depict proteins">.<br>
|
||
Labels for protein molecules that were generated at NCBI by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A> are shown as an alphanumeric combination, for example <IMG SRC="images/molecular_component_protein_circle_crystal_symmetry.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="Example of circle icons with alphanumeric labels used to depict protein molecules generated by applying transformations from crystallographic symmetry.">, indicating the source chain from which they were generated and the copy number.<BR><BR>
|
||
|
||
|
||
<A NAME="MmdbsrvProteinsMoleculeCount"></A><B>COUNT</B>: If you are viewing the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A>, the count reflects the number of protein molecules that were present in the PDB source file plus any copies that were generated by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>. If you are viewing the structure's <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, the count reflects only the number of molecules that were present in the PDB source file.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvProteinsMoleculeName"></A><B>MOLECULE</B>: The <B>name of the protein</B>, derived from the <B>COMPND</B> record of the PDB source file. <!-- The <B>name of the protein</B>, derived from the <B>_entity_pdbx_description</B> field of the mmCIF source file. --> If a particular protein name has been applied to multiple molecules (e.g., PDB chains A, B, etc.) within the PDB source file, those molecules are considered to be the same. A <B>non-redundant list of protein molecules</B> is then displayed, with the "count" column indicating the number of instances of each protein molecule in the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A> or <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, depending on what you are viewing in the current <A HREF="#MmdbsrvDisplayOptions">display</A>. Each protein molecule is represented with a <A HREF="#MmdbsrvProteinsShowAnnotation">sequence graph</A> and annotated with features such as <!-- A HREF="#MmdbsrvProteins3dDomains" -->3D domains and <!-- A HREF="#MmdbsrvProteinsClassification" -->domain families, as described below.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvProteinsGeneSymbols"></A><A NAME="MmdbsrvProteinsGeneSymbol"></A><A NAME="GeneSymbol"></A><A NAME="GeneID"></A><B>GENE</B>: A gene symbol, if/as available, appears beside the name of each protein molecule in the tabular list of <A HREF="#MolecularComponents">molecular components</A>. The protein-gene association is determined in the following way:<BR>
|
||
(1) The <A HREF="#SourceDatabases">source database</A>, PDB, provides a <A HREF="http://www.uniprot.org/">UniProt</A> ID for each protein chain in a structure record.<BR>
|
||
(2) The NCBI <A HREF="/gene">Gene database</A> generates data files on its <A HREF="//ftp.ncbi.nih.gov/gene/DATA/">FTP site</A> that provide mappings between protein identifiers and gene identifiers. Specifically: (a) the "gene_refseq_uniprotkb_collab.gz" file lists the correspondence between UniProt and <A HREF="/refseq/">RefSeq</A> protein accessions; and (b) the <!-- "gene2refseq.gz" --> "gene2accession.gz" file lists the correspondence between RefSeq protein accessions and Gene IDs. The <A HREF="#DataProcessing">MMDB data processing</A> pipeline creates a join between these two tables in order to map each UniProt ID to its corresponding Gene ID, and to link to the NCBI Gene record.<BR>
|
||
<I>(Note that the protein sequence in the structure record is not necessarily identical to the protein product of the gene. For example, a structure record might only contain a fragment of the protein rather than the whole protein. So there is a mapping between the structure's protein molecule and the gene product, but not necessarily an exact sequence match.)</I><BR><BR>
|
||
|
||
<!-- A NAME="MmdbsrvProteinsMoleculeInteractions"></A><B>INTERACTIONS</B>: A list of the other molecules in the structure with which this protein <A HREF="#DataProcessingInteractions">interacts</A> (i.e., with which it has <A HREF="#DataProcessingInteractionsContactNumberThreshold">at least 5 contacts</A> a distance of <A HREF="#DataProcessingInteractionsDistanceThreshold">4 Å or less</A> between the heavy atoms).[Å is the HTML code for Angstrom, <20>] This list can include the protein itself if there are multiple copies of that protein in the structure that interact with each other. {{Follow the "<B>explore interactions</B>" link to open a graphic that shows the specific points in the molecule that interact with other molecules.}}<BR><BR -->
|
||
|
||
<!-- ======= PROTEIN_THUMBNAIL_GRAPHIC_AND_FEATURE_ANNOTATIONS ======== -->
|
||
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" WIDTH="100%" CLASS="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD CLASS="format1H" COLSPAN="2" ALIGN="CENTER" VALIGN="TOP">
|
||
<A NAME="ProteinsAnnotationGraphic"></A>
|
||
<A NAME="MmdbsrvProteinsAnnotationGraphic"></A>
|
||
<A NAME="MmdbsrvProteinsShowAnnotation"></A>
|
||
<A NAME="MmdbsrvProteinsFeatureAnnotations"></A>
|
||
<A NAME="MmdbsrvProteinsThumbnail"></A>Protein annotation graphic<!-- Additional information and links for each protein molecule: --></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="140" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP"><A NAME="MmdbsrvProteinsSequenceGraph"></A>Sequence graph</TD>
|
||
<TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
|
||
The <B>sequence bar graph</B> for each protein molecule in the molecular components table <!-- of a <A HREF="#SummaryPage">structure record</A --> shows the protein's length in amino acids. Beneath that is an interactive graphic of the <B>geometrical and biological features</B> annotated on <!-- identified in --> the protein, such as <A HREF="#MmdbsrvProteins3dDomains">3D domains</A> and <A HREF="#MmdbsrvProteinsClassification">domain families</A> (protein classifications), respectively. For example, the illustration below shows the features annotated on the Prostaglandin H2 Synthase 1 protein, which is a component of the prostanglandin H2 synthase structure (<A HREF="/Structure/pdb/1PTH">1PTH</A>) from sheep. <B>Click</B> on the image to open the live MMDB structure summary record for <A HREF="/Structure/pdb/1PTH">1PTH</A>, which in turn includes a live, clickable protein annotation graphic:<!-- beside an individual protein molecule opens an interactive view of the 3D structure in <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A>, coloring the complete protein molecule or its 3D domains (if present) within the overall structure. The free <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> program (available for PC, Mac, or Unix) must be present on your computer in order for this to work.--><BR><BR>
|
||
|
||
<!-- UL>
|
||
<LI>The <B>"Protein" text link</B> in the interactive graphic opens the sequence record for that protein molecule in the <a HREF="/protein/">Entrez Protein</a> database</LI>
|
||
|
||
<LI>Click on the <B>sequence bar</B> in the interactive graphic to retrieve similar structures identified by the <a href="/Structure/VAST/vast.shtml">VAST</a> algorithm.</LI>
|
||
</UL -->
|
||
|
||
<A HREF="/Structure/pdb/1PTH"><IMG SRC="images/1PTH_molecular_components_protein_annotations.png" WIDTH="470" HEIGHT="260" BORDER="0" ALT="sample sequence graph showing the features annotated on the Prostaglandin H2 Synthase-1 protein, such as conserved domain families, which infer function, and 3D domains, which are compact substructures that are used to identify similar 3D structures. The protein is a component of the prostanglandin H2 synthase structure, 1PTH. Click on the image to open the MMDB structure summary record for 1PTH, which in turn includes a live, clickable protein annotation graphic"></A>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="140" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP"><A NAME="MmdbsrvProteins3dDomains"></A>3D Domains</TD>
|
||
<TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
|
||
<B>3D domains</B> are compact structural units within a protein that are identified automatically in MMDB using purely geometric criteria. A protein molecule can contain one or more 3D domains, which often correspond with <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains (<span style="color:#d70000">illustrated example</span>)</A> observed in molecular evolution. Additionally, proteins that are dissimilar in sequence might contain geometrically similar 3D domains, indicating a distant homology that cannot be recognized by sequence comparison. 3D domains are used in the identification of <!-- A HREF="#LinksSimilarStructures" --><!-- A HREF="#LinksRelatedStructures" --><!-- A HREF="#MmdbsrvRelatedStructures" --><A HREF="#MmdbsrvSimilarStructures">VAST Similar Structures</A>.<BR><BR>
|
||
|
||
<!-- The <B>"3D Domains" text link</B> {opens corresponding records in the <a HREF="/sites/entrez?db=domains">Entrez 3D Domains</a> database}. {Actually, that link opens the docsum view of the entire structure record; from there, a user would need to follow the Domains/3D Domains link to see the individual records for the 3D domains.}<BR><BR -->
|
||
|
||
The <B>Colored bars</B> in the "3D Domains" line in a protein molecule's sequence graph indicate the 3D domain boundaries. <!-- ALT: The <B>Colored bars</B> beneath an individual protein molecule in a <A HREF="#SummaryPage">structure record</A> indicate the 3D domain boundaries and are shown in the same color in the thumbnail 3D structure graphic of the protein molecule, which was generated by selecting "Color by domain" in the free <a HREF="/Structure/CN3D/cn3d.shtml">Cn3D</a> structure visualization program. --> <B>Click</B> on the bar for any 3D domain in the "show annotation" display to retrieve similar structures identified by the <A HREF="../../VAST/vast.shtml">VAST</A> algorithm.<BR><BR>
|
||
|
||
Note that a protein molecule can contain <B>one or more 3D domains</B>. A 3D domain may be composed of a <B>single region</B> of protein sequence, or <B>two or more non-contiguous regions</B> of the protein sequence. <BR><BR>
|
||
|
||
<B>If no compact substructures have been found</B> to exist within a protein molecule, then the overall molecule is regarded as a 3D domain in its own right. In that case, the <I>"3D Domains" line does not appear in the "show annotation graphic"</I> and you can click on the sequence bar itself to retrieve similar structures identified by the <A HREF="../../VAST/vast.shtml">VAST</A> algorithm. That will retrieve other structures similar in 3D shape of the overall protein molecule.<!-- and the overall molecule is shown in a color that corresponds to the thumbnail graphic -->.<BR><BR>
|
||
|
||
<I>(3D domains can also be seen in the interactive <!-- A HREF="#MmdbsrvDisplayOptions" -->3D structure view<!-- /A --> by displaying the structure in the free <A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A> web-based 3D viewer and selecting the menu option for "<B>Color > 3D Domain</B>", or by displaying the structure in the free <A HREF="../../CN3D/cn3d.shtml"><B>Cn3D</B></A> stand-alone software program and selecting the "<B>Style > Coloring Shortcuts > Domain</B>" option.)</I>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="140" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP"><A NAME="MmdbsrvProteinsClassification"></A>Domain Families<BR>(Protein classification)</TD>
|
||
<TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
|
||
The <B>"Domain Families" text link</B> in a protein molecule's sequence graph opens the <a HREF="/Structure/cdd/wrpsb.cgi">CD-Search</a> results for that protein sequence, showing the <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A> found in the protein, which infer protein function. These are the results of an <a href="../../cdd/cdd_help.shtml#CDSearch">RPS-BLAST</a> search of the protein molecule against the <a HREF="/cdd">Conserved Domain Database</a>.<BR><BR>
|
||
|
||
In contrast to 3D domains, the domain families are determined through the identification of blocks of amino acid residues (via <A HREF="../../cdd/cdd_help.shtml#CDModel">multiple sequence alignments</A>) that have been conserved across a broad range of taxonomic nodes and therefore represent recurring units of molecular evolution. The <a href="../../cdd/cdd_help.shtml">CDD help document</a> and <a href="../../cdd/cdd_help.shtml#CDSearch_help_contents">CD-Search help document</a> provide more details about <A HREF="../../cdd/cdd_help.shtml#CDWhat">conserved domains</A> and searching the database.<BR><BR>
|
||
|
||
<B>Mouse over</B> the <B>cartoon representing a conserved domain</B> for brief information about it, and <B>click</B> on the cartoon to open the corresponding, detailed record in the Conserved Domain Database. More details about each <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_types">type of conserved domain hit</A> are below:<BR>
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="140" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP"><P class="indent40"><A NAME="MmdbsrvProteinsClassificationSpecificHits"></A>Specific Hits</P></TD>
|
||
<TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">
|
||
A <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_specific_hit"><B>Specific Hit</B></A> meets or exceeds a domain-specific e-value threshold and represents a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model. Therefore, there is also a high confidence level for the inferred function of the protein query sequence. <I>(<A HREF="../../cdd/cdd_help.shtml#SpecificHit"><!-- FONT color="rgb(215,0,0)" --><span style="color:#d70000">Details and illustrations</span></A> are provided in the <A HREF="../../cdd/cdd_help.shtml#SpecificHit">Conserved Domain Database help document</A>.)</I>
|
||
</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="140" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP"><P class="indent40"><A NAME="MmdbsrvProteinsClassificationSuperfamilies"></A>Superfamilies</P></TD>
|
||
<TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">A <A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_superfamily"><B>Superfamily</B></A> is the domain cluster to which the specific and/or non-specific hits belong. This is a set of conserved domain models that generate overlapping annotation on the same protein sequences and are assumed to represent evolutionarily related domains. See additional details, including information about clustering methodology, in the <a href="../../cdd/cdd_help.shtml">CDD help document</a> section on "<A HREF="../../cdd/cdd_help.shtml#Superfamily">What is a superfamily?</A>"</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="140" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP"><P class="indent40"><A NAME="MmdbsrvProteinsClassificationMultidomains"></A>Multidomains</P></TD>
|
||
<TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP"><A HREF="../../cdd/cdd_help.shtml#RPSB_hit_type_multi_domain"><B>Multi-domains</B></A> are domain models that were computationally detected and are likely to contain multiple single domains. They are typically shown as <B>grey</B>-colored bars. (Examples are shown in the <A HREF="../../cdd/cdd_help.shtml#ConciseDisplay">concise display</A> and <A HREF="../../cdd/cdd_help.shtml#FullDisplay">full display</A> illustrations in the <a href="../../cdd/cdd_help.shtml#CDSearch_help_contents">CD-Search help document</a>.)</TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"> </TD>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP"> </TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- ======= END_PROTEIN_THUMBNAIL_GRAPHIC_AND_FEATURE_ANNOTATIONS ======== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ============ END_MOLECULAR_COMPONENTS_PROTEINS ========== -->
|
||
|
||
<!-- ============= MOLECULAR_COMPONENTS_NUCLEOTIDES ========== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" WIDTH="100" valign="top" style="white-space: nowrap;"><A NAME="MmdbsrvNucleotides"></A><A NAME="MmdbsrvMolecularComponentsNucleotides"></A><A NAME="MolecularComponentsNucleotides"></A><A NAME="MolecularComponentNucleotide"></A><B>Nucleotide Sequences</B><BR>(DNA or RNA)</TD>
|
||
<TD class="format1B" valign="top">
|
||
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
|
||
<A NAME="MmdbsrvNucleotidesDNAorRNA"></A>
|
||
<!-- B>DNA or RNA:</B> Nucleotide molecules can be DNA or RNA. Additional information about <A HREF="#DataTypeMolecularComponents">molecule types</A> is available in a separate section of this document.<BR><BR -->
|
||
|
||
<A NAME="MmdbsrvNucleotidesMoleculeLabel"></A><B>LABEL:</B>
|
||
Labels for nucleotide molecules are derived from their single letter chain codes (e.g., C, D) in the <A HREF="#SourceDatabases">PDB source file</A>. They are shown as square icons in the <A HREF="#MmdbsrvThumbnailSchematic">interaction schematic</A>, for example <IMG SRC="images/molecular_component_nucleotide_square.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="example of square icons used to depict nucleotide sequences">.<br>
|
||
Labels for nucleotide sequences that were generated at NCBI by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A> are shown as an alphanumeric combination, for example <IMG SRC="images/molecular_component_nucleotide_square_crystal_symmetry.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="Example of square icons with alphanumeric labels used to depict nucleotide sequences generated by applying transformations from crystallographic symmetry.">, indicating the source chain from which they were generated and the copy number.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvNucleotidesMoleculeCount"></A><B>COUNT</B>: If you are viewing the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A>, the count reflects the number of nucleotide molecules that were present in the PDB source file plus any copies that were generated by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>. If you are viewing the structure's <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, the count reflects only the number of molecules that were present in the PDB source file.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvNucleotidesMoleculeName"></A><B>MOLECULE</B>: The name of the nucleotide sequence, derived from the COMPND record of the PDB source file<!-- (and simply show the order of nucleotides in the molecule rather than an actual molecule name) -->, with the "count" column indicating the number of instances of each molecule in the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A> or <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, depending on what you are viewing in the current <A HREF="#SummaryPage">display</A>.<BR><BR>
|
||
|
||
<!-- A NAME="MmdbsrvNucleotidesMoleculeInteractions"></A><B>INTERACTIONS</B>: A list of the other molecules in the structure with which this nucleotide sequence <A HREF="#DataProcessingInteractions">interacts</A> (i.e., with which it has <A HREF="#DataProcessingInteractionsContactNumberThreshold">at least 5 contacts</A> a distance of <A HREF="#DataProcessingInteractionsDistanceThreshold">4 Å or less</A> between the heavy atoms).[Å is the HTML code for Angstrom, <20>] {{Follow the "<B>explore interactions</B>" link to open a graphic that shows the specific points in the molecule that interact with other molecules.}}<BR><BR -->
|
||
|
||
<!-- ======= NUCLEOTIDE_THUMBNAIL_GRAPHIC_AND_FEATURE_ANNOTATIONS ======== -->
|
||
|
||
<A NAME="MmdbsrvNucleotidesFeatureAnnotations"></A>
|
||
<TABLE style="margin:0px 0px 0px 0px;" WIDTH="100%" CLASS="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD CLASS="format1H" COLSPAN="2" ALIGN="CENTER" VALIGN="TOP"><A NAME="MmdbsrvNucleotidesThumbnail"></A>Bar graph for each nucleotide molecule: </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="140" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">Sequence graph</TD>
|
||
<TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">
|
||
<!-- A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A -->
|
||
The bar graph shown for each nucleotide sequence molecule in a <A HREF="#SummaryPage">structure record</A> shows the molecule's length in nucleotides. Follow the "<B>N Nucleotide</B>" text link (that appears to the left of the molecule's bar graph) to open the corresponding sequence record in the <a HREF="/sites/entrez?db=nuccore">Entrez Nucleotide</a> database.
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- ======= END_NUCLEOTIDE_THUMBNAIL_GRAPHIC_AND_FEATURE_ANNOTATIONS ======== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- =========== END_MOLECULAR_COMPONENTS_NUCLEOTIDES ========== -->
|
||
|
||
<!-- ========== MOLECULAR_COMPONENTS_CHEMICALS_LIGANDS ========= -->
|
||
|
||
<TR>
|
||
<TD class="format1H" WIDTH="100" valign="top" style="white-space: nowrap;"><A NAME="MmdbsrvChemicals"></A><A NAME="MmdbsrvMolecularComponentsChemicals"></A><A NAME="MolecularComponentsChemicals"></A><A NAME="MolecularComponentChemical"></A><B>Chemicals</B></TD>
|
||
<TD class="format1B" valign="top">
|
||
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
|
||
<!-- A <B>Chemical</B> section is present at the bottom of the <A HREF="#SummaryPage">structure summary page</A> if the 3D structure contains bound chemicals. The thumbnail graphics link to corresponding information about the physiochemical and biological properties of each chemical in the <A HREF="/pccompound/">PubChem Compound</A> or <A HREF="/pcsubstance/">PubChem Substance</A> database. These PubChem records have been associated with a structure using the method descibed in the <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A>/<A HREF="#DataProcessingDirectLinksSmallMolecules"><B>chemicals</B></A> section of this document.<BR><BR -->
|
||
|
||
<A NAME="MmdbsrvChemicalsMoleculeLabel"></A><B>LABEL</B>: If chemicals are present in the structure, they are shown as diamond-shaped icons in the <A HREF="#MmdbsrvThumbnailSchematic">interaction schematic</A> and labeled with integers, for example <IMG SRC="images/molecular_component_chemical_diamond.png" WIDTH="38" HEIGHT="15" BORDER="0" ALT="example of circle icons used to depict proteins">. If several chemicals have the same molecule name, they are labeled with the same number.<br>
|
||
If a chemical interacts only with a protein or nucleotide molecule that was generated by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>, then the chemical was also generated by crystallographic symmetry. Icon labels for chemicals generated by crystallographic symmetry include an underscore bar, with a number on either side of the underscore bar to indicate the source chemical and the copy number, respectively.
|
||
<!-- Labels for chemicals that were generated at NCBI by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A> contain two integers separated by an underscore bar, for example <IMG SRC="images/molecular_component_chemical_diamond_crystal_symmetry.png" WIDTH="38" HEIGHT="15" BORDER="0" ALT="Example of circle icons with alphanumeric labels used to depict protein molecules generated by applying transformations from crystallographic symmetry.">}}, indicating the source chain from which they were generated and the copy number. --><BR><BR>
|
||
|
||
|
||
<A NAME="MmdbsrvChemicalsMoleculeCount"></A><B>COUNT</B>: If you are viewing the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A>, the count reflects the number of chemicals that were present in the PDB source file plus any copies that were generated by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>. If you are viewing the structure's <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, the count reflects only the number of chemicals that were present in the PDB source file.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvChemicalsMoleculeName"></A><B>MOLECULE</B>: The name of the chemical, derived from from the HETNAM record of the PDB source file or from the <A HREF="/mesh">MeSH</A> terms associated with the corresponding <A HREF="https://pubchem.ncbi.nlm.nih.gov/">PubChem</A> Compound or Substance record. In order to provide a <B>non-redundant list of chemicals</B> found in the structure, the name of each unique chemical is listed only once. If two or more non-biopolymers were assigned the same HETNAM by PDB, the are grouped together under that name in the molecular components table. If their chemical structures are slightly different, they will be linked to separate <A HREF="https://pubchem.ncbi.nlm.nih.gov/">PubChem</A> substance IDs (SIDs). The "count" column indicates the number of instances of each chemical in the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A> or <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, reflecting what you are viewing in the current <A HREF="#SummaryPage">display</A>.<BR><BR>
|
||
|
||
<!-- A NAME="MmdbsrvChemicalsMoleculeInteractions"></A><B>INTERACTIONS</B>:
|
||
|
||
For chemicals, this column says "no interactions recorded" [[N/A (not applicable)]] because interactions are listed only for biopolymers (proteins and nucleotide sequences). Therefore, if a protein or nucleotide sequence molecule interacts with a chemical (if there are <A HREF="#DataProcessingInteractionsContactNumberThreshold">at least 5 contacts</A> a distance of <A HREF="#DataProcessingInteractionsDistanceThreshold">4 Å [Å is the HTML code for Angstrom, <20>] or less</A> between the heavy atoms), the chemical will be listed in the "Interactions" column for the corresponding biopolymer. The "explore interactions" link for the biopolymer will open a graphic display showing the amino acids or nucleotides that contact the chemical.<BR><BR>
|
||
|
||
A list of the other molecules in the structure with which this chemical <A HREF="#DataProcessingInteractions">interacts</A> (i.e., with which it has <A HREF="#DataProcessingInteractionsContactNumberThreshold">at least 5 contacts</A> a distance of <A HREF="#DataProcessingInteractionsDistanceThreshold">4 Å or less</A> between the heavy atoms).[Å is the HTML code for Angstrom, <20>] {{Follow the "<B>explore interactions</B>" link to open a graphic that shows the specific points in the molecule that interact with other molecules.}}<BR><BR -->
|
||
|
||
<A NAME="MmdbsrvChemicalsIons"></A>
|
||
<A NAME="MmdbsrvChemicalsCrystallizationAgents"></A>
|
||
<I>Note: <B>Ions</B> that <A HREF="#DataProcessingInteractions">interact</A> with the biomolecules in the structure but do not reach the <A HREF="#DataProcessingInteractionsContactNumberThreshold">5 contact threshold</A> will be absent from the <A HREF="#InteractionsSchematic">interaction schematic</A>; however, they will be listed in the tabular summary of <A HREF="#MolecularComponents">molecular components</A>. Interactions for <B>short peptides</B>, or for <B>molecule types other than protein, DNA/RNA, and chemical</B>, are not calculated. Molecules, such as <B>crystallization agents</B>, etc., that are not part of the biologically active molecule are absent from both the interaction schematic and the molecular components list.</I><BR><BR>
|
||
|
||
<!-- ======= CHEMICAL_THUMBNAIL_GRAPHIC_AND_FEATURE_ANNOTATIONS ======== -->
|
||
|
||
<A NAME="MmdbsrvChemicalsFeatureAnnotations"></A>
|
||
<TABLE style="margin:0px 0px 0px 0px;" WIDTH="100%" CLASS="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD CLASS="format1H" COLSPAN="2" ALIGN="CENTER" VALIGN="TOP"><A NAME="MmdbsrvChemicalsThumbnailGraphic"></A>Thumbnail image for each chemical: </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="140" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">Thumbnail graphic</TD>
|
||
<TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">
|
||
<!-- A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A -->
|
||
The thumbnail graphic for each chemical links to corresponding information about the physiochemical and biological properties of each chemical in the <A HREF="/pccompound/">PubChem Compound</A> or <A HREF="/pcsubstance/">PubChem Substance</A> database.<!-- These PubChem records have been associated with a structure using the method descibed in the <A HREF="#DataProcessing">data processing</A>/<A HREF="#DataProcessingDirectLinks">create direct links</A>/<A HREF="#DataProcessingDirectLinksSmallMolecules"><B>chemicals</B></A> section of this document. -->
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- ======= END_NUCLEOTIDE_THUMBNAIL_GRAPHIC_AND_FEATURE_ANNOTATIONS ======== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ========== END_MOLECULAR_COMPONENTS_CHEMICALS_LIGANDS ========= -->
|
||
|
||
<!-- ======= MOLECULAR_COMPONENTS_NON_STANDARD_BIOPOLYMERS ====== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" WIDTH="100" valign="top" style="white-space: nowrap;"><A NAME="MmdbsrvNonStandardBiopolymers"></A><A NAME="MmdbsrvMolecularComponentsNonStandardBiopolymers"></A><A NAME="MmdbsrvOther"></A><A NAME="MmdbsrvMolecularComponentsOther"></A><B>Non-standard Biopolymers</B></TD>
|
||
<TD class="format1B" valign="top">
|
||
|
||
<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
||
|
||
<A NAME="MmdbsrvNonStandardBiopolymersDefinition"></A><B>Non-standard biopolymers</B> are molecules such as nucleotide or protein sequences that contain a large percentage of non-standard residues. As an <B>example</B>, view the <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=4GLS">MMDB summary page for 4GLS</A>
|
||
"Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21."
|
||
<!-- (As an example, open the iCn3D display for <A HREF="/Structure/icn3d/full.html?&mmdbid=4GLS&bu=1&showanno=1&command=view+annotations;+set+annotation+cdd;+view+interactions">4GLS</A>.) --><BR><BR>
|
||
|
||
<A NAME="MmdbsrvNonStandardBiopolymersMoleculeLabel"></A><B>LABEL</B>: If non-standard biopolymers are present in the structure, they are shown as parallelograms in the <A HREF="#MmdbsrvThumbnailSchematic">interaction schematic</A> and labeled with letters, for example <IMG SRC="../../MMDB/docs/images/molecular_component_other_non_standard_biopolymers_parallelogram.png" WIDTH="34" HEIGHT="15" BORDER="0" ALT="example of parallelogram icons used to depict non-standard biopolymers">.
|
||
Labels for non-standard biopolymers that were generated at NCBI by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A> are shown as an alphanumeric combination, indicating the source molecule from which they were generated (to the left of the <b>underscore bar</b>) and the copy number (to the right of the underscore bar).
|
||
<BR><BR>
|
||
|
||
<A NAME="MmdbsrvNonStandardBiopolymersMoleculeCount"></A><B>COUNT</B>: If you are viewing the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A>, the count reflects the number of non-standard biopolymers that were present in the PDB source file plus any copies that were generated by applying transformations from <A HREF="#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>. If you are viewing the structure's <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, the count reflects only the number of non-standard biopolymers that were present in the PDB source file.<BR><BR>
|
||
|
||
<A NAME="MmdbsrvNonStandardBiopolymersMoleculeName"></A><B>MOLECULE</B>: The name of the non-standard biopolymer, derived from from the COMPND record of the PDB source file. In order to provide a <B>non-redundant list of non-standard biopolymers</B> found in the structure, the name of each unique chemical is listed only once. If two or more non-biopolymers were assigned the same COMPND by PDB, the are grouped together under that name in the molecular components table. The "count" column indicates the number of instances of each non-standard biopolymer in the structure's <A HREF="#DataProcessingBiologicalForms">biological unit</A> or <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, reflecting what you are viewing in the current <A HREF="#SummaryPage">display</A>.<BR><BR>
|
||
|
||
<!-- A NAME="MmdbsrvNonStandardBiopolymersMoleculeInteractions"></A><B>INTERACTIONS</B>:
|
||
|
||
A list of the other molecules in the structure with which this non-standard biopolymer <A HREF="#DataProcessingInteractions">interacts</A> (i.e., with which it has <A HREF="#DataProcessingInteractionsContactNumberThreshold">at least 5 contacts</A> a distance of <A HREF="#DataProcessingInteractionsDistanceThreshold">4 Å or less</A> between the heavy atoms).[Å is the HTML code for Angstrom, <20>] {{Follow the "<B>explore interactions</B>" link to open a graphic that shows the specific points in the molecule that interact with other molecules.}}<BR><BR -->
|
||
|
||
<!-- ======= NON_STANDARD_BIOPOLYMER_THUMBNAIL_GRAPHIC ======== -->
|
||
|
||
<!-- A NAME="MmdbsrvNonStandardBiopolymersFeatureAnnotations"></A>
|
||
<TABLE style="margin:0px 0px 0px 0px;" WIDTH="100%" CLASS="format1 TableText1">
|
||
|
||
<TR>
|
||
<TD CLASS="format1H" COLSPAN="2" ALIGN="CENTER" VALIGN="TOP"><A NAME="MmdbsrvNonStandardBiopolymerThumbnailGraphic"></A>Thumbnail image for each chemical: </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="140" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">Thumbnail graphic</TD>
|
||
<TD CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">
|
||
[<A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>]
|
||
The thumbnail graphics link to corresponding information about the molecule in the <A HREF="/protein/">Protein</A> or <A HREF="/nuccore/">Nucleotide</A> database.
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR -->
|
||
|
||
<!-- ======= END_NON_STANDARD_BIOPOLYMER_THUMBNAIL_GRAPHIC ======== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ======= END_MOLECULAR_COMPONENTS_NON_STANDARD_BIOPOLYMERS ====== -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top" style="white-space: nowrap;"><A NAME="_____"><B>Object Name</B></A></TD>
|
||
<TD class="format1B" valign="top">Description with <A HREF="#____">anchor</A> to other part of document.</TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
|
||
<!-- ================= END_MOLECULAR_COMPONENTS_DETAILS ============== -->
|
||
|
||
<BR>
|
||
|
||
<!-- B>*</B> The "_____" and "_____" objects are found only on the <A HREF="#____">____ page</A>. They are not present in the "<A HREF="#_____">_____</A>" display. -->
|
||
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- =================== END_MOLECULAR_COMPONENTS ================ -->
|
||
|
||
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_6_CONTENTS ====== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_6_CONTENTS ############ -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ################## BLUE_HEADER_SECTION_7 ######################## -->
|
||
|
||
<A NAME="WebAPI"></A>
|
||
<A NAME="MmdbsrvStructureViewURLformat"></A>
|
||
<A NAME="StructureViewURLformat"></A>
|
||
<A NAME="URLformat"></A>
|
||
<A NAME="MmdbsrvStructureViewWebAPI"></A>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1"><B>Web API</B></SPAN></TD>
|
||
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ################## END_BLUE_HEADER_SECTION_7 ######################## -->
|
||
|
||
|
||
<!-- ############## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_7_CONTENTS ########### -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
||
<TR>
|
||
<TD class="WhiteCellBlueEdgeAll">
|
||
|
||
<!-- ====== LEVEL_1_WEB_API_DISPLAY_OPTIONS_URL_FORMAT_URL_SYNTAX ======= -->
|
||
|
||
<BR>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Web API:  URL format for displaying or saving a structure record:</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A><BR><BR>
|
||
|
||
It is possible to view or save a 3D structure record by linking directly to it. The URL format, parameters, and allowable values, are as follows:
|
||
</P>
|
||
|
||
<!-- =========== LEVEL_2_TABLE_CITING_ONLY_STRUCTURE_DB ============== -->
|
||
|
||
<!-- ============ MINI_TOC FOR URL_FORMAT_URL_SYNTAX ============== -->
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<A HREF="#StructureViewURLformatBaseURL">base URL</A> | <A HREF="#StructureViewURLformatParameters">parameters & allowable values</A> (<A HREF="#StructureViewURLformatParameterUid">uid</A>, <A HREF="#StructureViewURLformatParameterBuidx">buidx</A>, <A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A>, <A HREF="#StructureViewURLformatParameterDisplay">display</A>, <A HREF="#StructureViewURLformatParameterComplexity">complexity</A>) | <A HREF="#StructureViewURLformatExamples">examples of URLs for displaying or saving 3D structure records</A>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============ END MINI_TOC FOR URL_FORMAT_URL_SYNTAX ============== -->
|
||
|
||
<UL>
|
||
|
||
<!-- ============ URL_FORMAT_URL_SYNTAX_BASE_URL ============== -->
|
||
|
||
<LI><A NAME="StructureViewURLformatBaseURL"></A><A NAME="URLformatBaseURL"></A>base URL: <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></LI>
|
||
|
||
<!-- === BASE URL TABLE FORMAT_B === -->
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" CLASS="format1 NormalText">
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><B>/Structure/mmdb/mmdb_strview.cgi?</B></TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============ URL_FORMAT_URL_SYNTAX_PARAMETERS ============== -->
|
||
|
||
<LI><A NAME="StructureViewURLformatParameters"><A NAME="StructureViewURLformatParameter"><A NAME="URLformatParameters"></A><A NAME="URLformatParameter"></A>parameters and allowable values:</A> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></LI>
|
||
|
||
<!-- === PARAMETERS: TABLE FORMAT_B === -->
|
||
|
||
<BLOCKQUOTE>
|
||
<TABLE style="margin:0px 0px 0px 0px;" CLASS="format1 NormalText">
|
||
|
||
<!-- === PARAMETERS: UID === -->
|
||
|
||
<!-- TR>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP" COLSPAN="2"><A NAME="StructureViewURLformatParameterIdentifiers"></A>To specify the structure record you want to view:</TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="StructureViewURLformatParameterUid"></A><A NAME="URLformatParameterUid"></A><B>uid</B></TD>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">Specify the structure record you want to retrieve by entering either its <A HREF="#MmdbsrvMMDBID">MMDB ID</A> or <A HREF="#MmdbsrvPDBID">PDB ID</A>. The PDB ID can be either lowercase or uppercase.</TD>
|
||
</TR>
|
||
|
||
<!-- === PARAMETERS: BUIDX === -->
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="StructureViewURLformatParameterBuidx"></A><A NAME="URLformatParameterBuidx"></A><B>buidx</B></TD>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">Specify whether you want to see the structure's <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, the default <A HREF="#DataProcessingBiologicalForms">biological unit</A> (biounit), or other biological units (if present). The <B>allowable values</B> are:<BR><BR>
|
||
|
||
<B>0</B> = <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A><BR>
|
||
<B>1</B> = default <A HREF="#DataProcessingBiologicalForms">biological unit</A><BR>
|
||
<B>2</B> = second biological unit (if present in the structure record)<BR>
|
||
<B>N</B> = N<sup>th</sup> biological unit.<BR><BR>
|
||
|
||
<B>Default:</B>  If the buidx parameter is not included in the URL, a "buidx" value of "1" will be applied (i.e., the default biounit will be returned).<BR><BR></TD>
|
||
</TR>
|
||
|
||
<!-- === PARAMETERS: FILEFORMAT === -->
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="StructureViewURLformatParameterProgram"></A><A NAME="URLformatParameterProgram"></A><A NAME="StructureViewURLformatParameterFileFormat"></A><A NAME="URLformatFileFormat"></A><B>fileformat</B></TD>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">Specify the desired file format for viewing the structure. The <B>allowable values</B> can be written in either lowercase or uppercase and are as follows:<BR><BR>
|
||
|
||
<B>cn3d</B> = This option renders the data in <A HREF="../../asn1.html">ASN.1 format</A>, which enables you to view the data in NCBI's free <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> structure viewing program.<!-- A separate part of this help document provides <A HREF="#MmdbsrvStructureViewFileFormatCn3D">more information about the Cn3D option,</A --> Cn3D allows examination of <A HREF="#DataProcessingBiologicalForms">biological units</A>, <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric units</A>, and <A HREF="#DatabaseApplications">sequence-structure relationships</A>, and allows <A HREF="#EvolutionaryRelationships">superposition</A> of geometrically similar structures.<BR><BR>
|
||
|
||
<B>pdb</B> = This option renders the data in <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB format</A>, which enables you to view the data in programs such as <A HREF="http://www.umass.edu/microbio/rasmol/">Rasmol</A> and other 3D structure viewers that accept PDB file format.<!-- (You can also specify "rasmol" instead of "pdb" for this parameter and the result will be the same.) --><!-- A separate part of this help document provides more information about the <A HREF="#MmdbsrvStructureViewFileFormatPDB">PDB</A> option. -->
|
||
|
||
<BLOCKQUOTE>
|
||
<I>Note, however, that the saved PDB file may be somewhat different from the original <A HREF="#SourceDatabases">PDB source file</A>, due to content validation procedures applied during <A HREF="#DataProcessing">MMDB data processing</A>. These differences are explained in a separate section of this document on "<A HREF="#MmdbsrvSave">saving a struture record</A> > <A HREF="#MmdbsrvSavePDBformat">PDB format</A> > <A HREF="#MmdbsrvSavePDBformatDetails">details about the data that are saved</A>."<BR><BR>
|
||
|
||
To save an exact copy of the original <A HREF="#SourceDatabases">PDB source file</A>, use the parameters of "<A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A>=pdb" AND "<A HREF="#StructureViewURLformatParameterComplexity">complexity</A>=4". In such case, the "<A HREF="#StructureViewURLformatParameterBuidx">buidx</A>" argument will be ignored. For other "complexity" input values, the cgi will create an NCBI-style PDB formatted data set with "complexity=3" only (all atoms), and with whatever "buidx" value you specify.</I>
|
||
|
||
<!-- To save an exact copy of the original <A HREF="#SourceDatabases">PDB source file</A>, click on the "Download" button that appears next to the PDB ID in the upper right hand corner of a <A HREF="#SummaryPage">structure summary page</A>. -->
|
||
<!-- To save an exact copy of the original <A HREF="#SourceDatabases">PDB source file</A>, display the asymmetric unit and select "File Format: PDB" + "<A HREF="#MmdbsrvStructureViewDataSet">Data Set</A>: <A HREF="#MmdbsrvStructureViewDataSetPDBdataset">PDB data set</A>." -->
|
||
</BLOCKQUOTE>
|
||
|
||
<B>xml</B> = This option renders the data in <A HREF="/IEB/ToolBox/XML/ncbixml.txt">XML format</A>.<BR>
|
||
If you specify this fileformat, the only <A HREF="#StructureViewURLformatParameterDisplay">display</A> options available are "1" (save data to a file) and "2" (see data in web browser, which is the default display for XML format).<BR><BR>
|
||
|
||
<B>json</B> = This option renders the data in <A HREF="http://json.org/">JSON format</A>.<BR>
|
||
If you specify this fileformat, the only <A HREF="#StructureViewURLformatParameterDisplay">display</A> options available are "1" (save data to a file) and "2" (see data in web browser, which is the default display for JSON format).<BR><BR>
|
||
|
||
<B>Default:</B>  If the "fileformat" parameter is not included in the URL, the <B>cn3d</B> (ASN.1) file format will be returned by default. A separate section of this document provides <A HREF="#MmdbsrvStructureViewFileFormat">additional details about file formats</A>.<BR><BR>
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- === PARAMETERS: DISPLAY === -->
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="StructureViewURLformatParameterDisplay"></A><A NAME="URLformatParameterDisplay"></A><B>display</B></TD>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">Specify what you would like the browser to do with the file. The <B>allowable values</B> are:<BR><BR>
|
||
|
||
<B>0</B> = launch the <!-- A HREF="../../CN3D/cn3d.shtml">Cn3D</A --> structure viewer, automatically opening the file in that program so you can view the structure interactively.
|
||
|
||
<BLOCKQUOTE>
|
||
<I>Note that the structure viewer you will use (e.g., NCBI's free <a href="../../CN3D/cn3d.shtml"><B>Cn3D</B></a> program or a PDB-format compatible viewer) must be <A HREF="../../CN3D/cn3dinstall.shtml"><B>installed</B></A> on your computer and <B><A HREF="../../CN3D/cn3dinstall.shtml#browser"><B>configured</B></A> as a helper application</B> for your browser in order for the display parameter of "0" to automatically open the 3D structure. If you already have Cn3D 4.1 or earlier on your computer, you will need to <B>upgrade to Cn3D 4.3</B> (<A HREF="../../CN3D/cn3dinstall.shtml">install</A>) in order to view 3D structures that were reconstructed by applying transformations from <A HREF="#DataProcessingCrystalSymmetry">crystallographic symmetry</A>.</I>
|
||
</BLOCKQUOTE>
|
||
|
||
<B>1</B> = save data to a file<BR><BR>
|
||
|
||
<B>2</B> = see data in the web browser<BR>
|
||
|
||
<!-- B>3</B> = display <A HREF="../../asn1.html">ASN.1 format</A> data as plain text<BR>
|
||
|
||
<B>4</B> = display <A HREF="/IEB/ToolBox/XML/ncbixml.txt">XML format</A> data in web browser.<BR>(This option is available only when the <A HREF="#StructureViewURLformatParameterProgram">program parameter</A> is set to <B>cn3d</B>.)<BR>
|
||
|
||
<B>5</B> = display <A HREF="http://json.org/">JSON format</A> data in web browser.<BR>(This option is available only when the <A HREF="#StructureViewURLformatParameterProgram">program parameter</A> is set to <B>cn3d</B>.)<BR><BR -->
|
||
|
||
<BLOCKQUOTE>
|
||
<I>Note: If you specify "xml" or "json" for the "fileformat" parameter, the only display options available are "1" (save data to a file) and "2" (see data in web browser, which is the default display for xml and json format.</I>
|
||
</BLOCKQUOTE>
|
||
|
||
<B>Defaults:</B>  If the <A HREF="#StructureViewURLformatParameterDisplay">display</A> parameter is not included in the URL, the value of <B>0 (launch structure viewer)</B> will be used by default if the <A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A> parameter is set to <B>"cn3d" or "pdb"</B>. The display value of "2" (see data in web browser) will be used by default if the fileformat parameter is set to either <B>"xml" or "json"</B>.<BR><BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- === PARAMETERS: COMPLEXITY === -->
|
||
|
||
<!-- TR>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP" COLSPAN="2"><A NAME="StructureViewURLformatParameterDataSet"></A>To specify the desired <A HREF="#MmdbsrvStructureViewDataSet">data set</A> (complexity) of the structure:</TD>
|
||
</TR -->
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="StructureViewURLformatParameterDataSet"></A><A NAME="URLformatParameterDataSet"></A><A NAME="StructureViewURLformatParameterComplexity"></A><A NAME="URLformatParameterComplexity"></A><B>complexity</B></TD>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">Specify the desired complexity (<A HREF="#MmdbsrvStructureViewDataSet">data set</A>) of the structure you want to view. The allowable values are:<BR><BR>
|
||
|
||
<B>1</B> = <!-- A HREF="#MmdbsrvStructureViewDataSetVector" -->vector<!-- /A -->. This option is valid if <A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A>=cn3d or xml or json. It returns data about the secondary structures identified in the asymmetric unit or biological unit, and their orientation (vector) in 3D space.<BR><BR>
|
||
|
||
<B>2</B> = <A HREF="#MmdbsrvStructureViewDataSetBackbone">backbone</A> (alpha carbons). This option is valid if <A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A>=cn3d or xml or json.<BR><BR>
|
||
|
||
<B>3</B> = <A HREF="#MmdbsrvStructureViewDataSetAllAtoms">all atoms</A> (single 3D structure). This option is valid for all <A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A> values.<BR><BR>
|
||
|
||
<!-- B>__</B> = <A HREF="#MmdbsrvStructureViewDataSetAllModels">all models</A> (all 3D structures; all members of NMR ensembles or correlated disorder sets from crystallography)<BR><BR -->
|
||
|
||
<B>4</B> = <A HREF="#MmdbsrvSavePDBformatDetails"><!-- A HREF="#MmdbsrvStructureViewDataSetPDBdataset" -->PDB model</A>. This option is valid only if <A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A>=pdb.<BR>
|
||
If fileformat=pdb and complexity=4, the program will return the original <A HREF="#SourceDatabases">PDB source file</A>. In that case, the only available biounit value is <A HREF="#StructureViewURLformatParameterBuidx">buidx</A>=0 (<A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>); that value will be applied regardless of whether you insert any other value.<BR><BR>
|
||
|
||
<B>Default:</B>  If the complexity parameter is not included in the URL, the value of <B>3 (all atoms)</B> will be used by default.<BR><BR>
|
||
|
||
If a structure has >25,000 atoms, the value of <B>2 (backbone)</B> is selected by default. If a structure record contains an <A HREF="#DataTypeExperimentalMethods">NMR</A> ensemble or a correlated disorder set from crystallography, this will download backbone data only for the first model in the set.<BR><BR>
|
||
|
||
If the "<A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A>" parameter is set to "pdb," the only complexity values available are <B>3 (all atoms)</B> and <B>4 (PDB model)</B>; if any other number is specified, it will be invalid and will be set to <B>3</B>.
|
||
<!-- Additionally, if fileformat=pdb and complexity=4, the only available biounit value is buidx=0 (<A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>); that value will be applied regardless of whether you insert any other value. --><BR><BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP" COLSPAN="2"><A NAME="StructureViewURLformatParameter_________"></A>to do ___________:</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP"><A NAME="StructureViewURLformatParameter________"></A><B>_____</B></TD>
|
||
<TD WIDTH="___" CLASS="format1A" ALIGN="LEFT" VALIGN="TOP">____________________________________________.</TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<LI><A NAME="StructureViewURLformatExamples"></A><A NAME="URLformatExamples"></A>examples of URLs for <A HREF="#MmdbsrvStructureView">displaying or saving 3D structure records</A>: <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></LI>
|
||
|
||
<!-- === URL FORMAT EXAMPLE1: TABLE FORMAT_B === -->
|
||
|
||
<A NAME="StructureViewURLformatExample1"></A>
|
||
<A NAME="URLformatExample1"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<B>Example #1:</B> Retrieve the 1LFL (Deoxy Hemoglobin, 90% Relative Humidity) structure record's default <A HREF="#DataProcessingBiologicalForms">biological unit</A> ("<A HREF="#StructureViewURLformatParameterBuidx">buidx</A>=1") in cn3d (ASN.1) <A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A>, then <A HREF="#StructureViewURLformatParameterDisplay">display</A> the structure in the Cn3D program, with a <A HREF="#StructureViewURLformatParameterComplexity">complexity</A> that shows all atoms:<BR><BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" CLASS="format1 NormalText">
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="/Structure/mmdb/mmdb_strview.cgi?uid=1LFL&buidx=1&fileformat=cn3d&display=0&complexity=3"> /Structure/mmdb/mmdb_strview.cgi?uid=1LFL&buidx=1&fileformat=cn3d&display=0&complexity=3</A>
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<BLOCKQUOTE>
|
||
<I>Note: If desired, the "<A HREF="#StructureViewURLformatParameterComplexity">complexity</A>" parameter can be omitted from the URL, because the default complexity value is "3."</I>
|
||
</BLOCKQUOTE>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
|
||
<!-- === URL FORMAT EXAMPLE2: TABLE FORMAT_B === -->
|
||
|
||
<A NAME="StructureViewURLformatExample2"></A>
|
||
<A NAME="URLformatExample2"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<B>Example #2:</B> Retrieve the 1LFL (Deoxy Hemoglobin, 90% Relative Humidity) structure record's <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A> ("<A HREF="#StructureViewURLformatParameterBuidx">buidx</A>-=0") in <!-- A HREF="http://www.wwpdb.org/docs.html"><A HREF="http://www.wwpdb.org/documentation/file-format" -->PDB <A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A>, then <A HREF="#StructureViewURLformatParameterDisplay">display</A> the file in the web browser, showing the coordinates for all atoms ("<A HREF="#StructureViewURLformatParameterComplexity">complexity</A>=3").<!-- Because the complexity parameter is not included in the URL, the default value of 3 (all atoms) will be applied: --><BR><BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" CLASS="format1 NormalText">
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="/Structure/mmdb/mmdb_strview.cgi?uid=1LFL&buidx=0&fileformat=pdb&display=2&complexity=3">/Structure/mmdb/mmdb_strview.cgi?uid=1LFL&buidx=0&fileformat=pdb&display=2&complexity=3</A>
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<BLOCKQUOTE>
|
||
<I>Note that the saved PDB-format file returned by the URL above may be somewhat different from the original <A HREF="#SourceDatabases">PDB source file</A>, due to content validation procedures applied during <A HREF="#DataProcessing">MMDB data processing</A>. These differences are explained in a separate section of this document on "<A HREF="#MmdbsrvSave">saving a struture record</A> > <A HREF="#MmdbsrvSavePDBformat">PDB format</A> > <A HREF="#MmdbsrvSavePDBformatDetails">details about the data that are saved</A>." If you would like to view/download a copy of the original <A HREF="#SourceDatabases">PDB source file</A>, use the URL parameters shown in the next example.</I>
|
||
|
||
<!-- I>To save an <B>exact copy of the original</B> <A HREF="#SourceDatabases"><B>PDB source file</B></A>, use the parameters of "fileformat=pdb" (or "fileformat=rasmol") AND "complexity=4". In such case, the "buidx" argument will be ignored. (Since the PDB source file contains the <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A> ("buidx=0"), that is the only thing that can be returned.) For other "complexity" input values, the cgi will create an NCBI-style PDB formatted data set with "complexity=3" only (all atoms), and with whatever "buidx" value you specify. --></I -->
|
||
|
||
<!-- To save an exact copy of the original <A HREF="#SourceDatabases">PDB source file</A>, display the asymmetric unit and select "File Format: PDB" + "<A HREF="#MmdbsrvStructureViewDataSet">Data Set</A>: <A HREF="#MmdbsrvStructureViewDataSetPDBdataset">PDB data set</A>." -->
|
||
</BLOCKQUOTE>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
|
||
<!-- === URL FORMAT EXAMPLE3: TABLE FORMAT_B === -->
|
||
|
||
<A NAME="StructureViewURLformatExample3"></A>
|
||
<A NAME="URLformatExample3"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<B>Example #3:</B> Retrieve the <B>original</B> <A HREF="#SourceDatabases"><B>PDB source file</B></A> for the 1LFL (Deoxy Hemoglobin, 90% Relative Humidity) structure record, by using the parameters of "<A HREF="#StructureViewURLformatParameterFileFormat">fileformat</A>=pdb" AND "<A HREF="#StructureViewURLformatParameterComplexity">complexity</A>=4".<BR><BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" CLASS="format1 NormalText">
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="/Structure/mmdb/mmdb_strview.cgi?uid=1LFL&fileformat=pdb&display=2&complexity=4">/Structure/mmdb/mmdb_strview.cgi?uid=1LFL&fileformat=pdb&display=2&complexity=4</A>
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<BLOCKQUOTE>
|
||
<I>Note: When the parameters of "fileformat=pdb" and "complexity=4" are used together, the "<A HREF="#StructureViewURLformatParameterBuidx">buidx</A>" argument is ignored. For this reason, the "buidx" parameter is not included in the sample URL above. This is because the original <A HREF="#SourceDatabases">PDB source file</A> contains the <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>, so that is the only thing that can be returned<!-- (i.e., "buidx-0" is the only valid value and is therefore applied by default) -->.</I>
|
||
</BLOCKQUOTE>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- === URL FORMAT EXAMPLE__: TABLE FORMAT_B === -->
|
||
|
||
<A NAME="StructureViewURLformatExample__"></A>
|
||
<A NAME="URLformatExample__"></A>
|
||
|
||
<!-- BLOCKQUOTE>
|
||
|
||
<B>Example #__:</B> Retrieve the ___ (_____________) structure record's [<A HREF="#DataProcessingBiologicalForms">biological unit</A> | <A HREF="#DataProcessingBiologicalFormsAdditionalNotes">asymmetric unit</A>] in ____ format, then save the data to a file, with a complexity that includes [only alpha carbons (backbone) | all atoms]. [Because the ____ parameter is not included in the URL, the default value of ____ will be applied:]<BR><BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" CLASS="format1 NormalText">
|
||
|
||
<TR>
|
||
<TD WIDTH="___" CLASS="format1H" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="______">/Structure/mmdb/mmdb_strview.cgi?uid=____&buidx=__&fileformat=__&display=__&complexity=__</A>
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR -->
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_CONTENTS ====== -->
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ############### END_BLUE_EDGE_BOX_WITH_SECTION_7_CONTENTS ############ -->
|
||
|
||
<!-- ==================== VERTICAL SPACER ======================= -->
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
<TR>
|
||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ==================== END_VERTICAL SPACER ======================= -->
|
||
|
||
<!-- ################## BLUE_HEADER_SECTION_8 ######################## -->
|
||
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<A NAME="References"></A>
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<TD class="SteelBlueCell"><SPAN class="HeaderText1">References</SPAN></TD>
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<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
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<!-- ================= LEVEL_1_REFERENCES_CITING ==================== -->
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<A NAME="Citing"></A>
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<BR><BR>
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<P class="indent20">
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<SPAN class="HeaderText3"><B>Citing the Molecular Modeling Database:</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
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<!-- =========== LEVEL_2_TABLE_CITING_ONLY_STRUCTURE_DB ============== -->
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<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="4" class="ReferenceText">
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<TD width="18" valign="top" align="left"><A NAME="MMDB_NAR_2014"></A><A HREF="/pubmed/24319143?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
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<TD valign="top" align="left"><A HREF="/pubmed/24319143?dopt=AbstractPlus">Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. MMDB and VAST+: tracking structural similarities between macromolecular complexes. <B><I>Nucleic Acids Res.</I> 2014</B> Jan 1;42(1):D297-303. Epub 2013 Dec 6. doi: 10.1093/nar/gkt1208. [PubMed PMID: 24319143]</A> <A HREF="http://nar.oxfordjournals.org/content/42/D1/D297.long"><!-- A HREF="http://nar.oxfordjournals.org/content/early/2013/12/05/nar.gkt1208.full" -->[Full Text]</A></TD>
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<!-- TR>
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<TD width="18" valign="top" align="left"><A NAME="MMDB_NAR_2012"></A><A HREF="/pubmed/22135289?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
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<TD valign="top" align="left"><A HREF="/pubmed/22135289?dopt=AbstractPlus">Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH. MMDB: 3D structures and macromolecular interactions. <B><I>Nucleic Acids Res.</I> 2012</B> Jan; 40(1):D461-4. Epub 2011 Dec 1. [PubMed PMID: 22135289]</A> <A HREF="http://nar.oxfordjournals.org/content/40/D1/D461.long">[Full Text]</A></TD>
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</TR -->
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<!-- TR>
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<TD width="18" valign="top" align="left"><A NAME="MMDB_NAR_2007"></A><A HREF="/pubmed/17135201?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
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<TD valign="top" align="left"><A HREF="/pubmed/17135201?dopt=AbstractPlus">Wang Y, Addess KJ, Chen J, Geer LY, He J, He S, Lu S, Madej T, Marchler-Bauer A, Thiessen PA, Zhang N, Bryant SH. MMDB: annotating protein sequences with Entrez's 3D-structure database. <B><I>Nucleic Acids Res.</I> 2007</B> Jan; 35(Database issue): D298-300.</A></TD>
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</BLOCKQUOTE>
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<!-- ======== LEVEL_1_REFERENCES_CITING_SPECIFIC_STRUCTURE_RECORD ========= -->
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<!-- A NAME="CitingMMDBRecord"></A>
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<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Citing an individual MMDB record:</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
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</P -->
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<!-- ======= LEVEL_2_TABLE_CITING_SPECIFIC_STRUCTURE_RECORD_EXAMPLE ========= -->
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<!-- A NAME="CitingMMDBRecordExample"></A>
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||
<BLOCKQUOTE>
|
||
If you are citing a particular record from the MMDB, it is appropriate to cite both that database and the source database (using the citation suggested on the web site of the source database). For example, the MMDB record for _____ (<A HREF="/____">____</A>) could be cited in the following way:<BR><BR>
|
||
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||
...The list of human genes involved in arachidonic acid metabolism was obtained from the NCBI BioSystems Database record BSID82991 (1), based on the KEGG record hsa00590 (2)...
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<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="4" class="ReferenceText">
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<TD width="18" valign="top" align="left"><A NAME="CitingBSID82991">(1)</TD>
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||
<TD valign="top" align="left"><A HREF="/biosystems/82991">NCBI BioSystems Database [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information. 2009 - Record No. 82991, Arachidonic acid metabolism; [cited 2009 Mar 11]; [about 1 screen]. Available from: /biosystems/82991</A></TD>
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<TR>
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<TD width="18" valign="top" align="left"><A NAME="CitingKEGGhsa00590">(2)</TD>
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||
<TD valign="top" align="left"><A HREF="http://www.genome.jp/dbget-bin/show_pathway?hsa00590">KEGG: Kyoto Encyclopedia of Genes and Genomes. Kyoto, Japan: Kyoto University, Institute for Chemical Research, Bioinformatics Center, Kanehisa Laboratory. 1995 - Record No. hsa00590, Arachidonic acid metabolism; [cited 2009 Mar 11]; [about 1 screen]. Available from: http://www.genome.jp/dbget-bin/show_pathway?hsa00590</A></TD>
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<BR>
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</BLOCKQUOTE -->
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<!-- ================= LEVEL_1_REFERENCES_ADDITIONAL ==================== -->
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||
<A NAME="____"></A>
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||
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<P class="indent20">
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||
<SPAN class="HeaderText3"><B>Additional References:</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
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</P>
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||
<!-- ============== LEVEL_2_TABLE_OF_REFERENCES_ADDITIONAL ================= -->
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<A NAME="ReferencesAdditional"></A>
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<BLOCKQUOTE>
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<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="4" class="ReferenceText">
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<TR>
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<TD width="18" valign="top" align="left"><A HREF="mmdb_publications.html"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
||
<TD valign="top" align="left"><A HREF="mmdb_publications.html">Additional articles are noted on the <B>publications page</B> for the Molecular Modeling Database.</A></TD>
|
||
</TR>
|
||
|
||
<!-- TR>
|
||
<TD width="18" valign="top" align="left"><A NAME="_____"></A><A HREF="/pubmed/_______?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
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||
<TD valign="top" align="left"><A HREF="/pubmed/_______?dopt=AbstractPlus">____authors_title_journal_etc___</A></TD>
|
||
</TR -->
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<TD width="18" valign="top" align="left"><A NAME="_____"></A><A HREF="/pubmed/_______?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
||
<TD valign="top" align="left"><A HREF="/pubmed/_______?dopt=AbstractPlus">____authors_title_journal_etc___</A></TD>
|
||
</TR -->
|
||
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<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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<TD class="WhiteCell NormalText"> </TD>
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<!-- =================== PAGE_FOOTER_AND_DATE_REVISED ================== -->
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 16 August 2021</SPAN></TD>
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