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<meta name="keywords" content="VAST+, VAST Plus, Vector Alignment Search Tool (VAST), 3D macromolecular structures, three-dimensional structures, 3D, 3-D, structural alignments, similar structures, superpose, superpositions, superimpose, superimposition, proteins, chemicals, nucleotide sequences, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, nucleic acids, DNA, RNA, ligands, bound chemicals, drugs, medicine, Entrez Structure, Molecular Modeling Database (MMDB), Conserved Domains Database (CDD), CDTree, CD Tree, PubChem, NCBI, National Center for Biotechnology Information" />
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<TD class="DocTitleText" align="left"> <A HREF="../vastplus.cgi">VAST+  Help Document<!-- SPAN class="DocTitleTextSmall13">Vector Alignment Search Tool</SPAN --></A></TD>
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<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="vastplus_about.html"> ABOUT </A></TD -->
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A HREF="../vastplus.cgi"> SEARCH </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../../VAST/docs/vast_publications.html"> PUBLICATIONS </A></TD>
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<SPAN class="MiniText"> <BR></SPAN>
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<P class="indent20bottomspace">This help document describes how to use <A HREF="../vastplus.cgi"><B>VAST+</B></A>, an enhanced version of VAST that finds macromolecular structures that are similar in 3D shape, and groups them as complete or partial matches to the <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit"><B>biological unit</B> ("<B>biounit</B>")</A> of a query structure, making it possible to find similar macromolecular complexes.<!-- It includes detailed descriptions of input required, output displays, and the program's features and functions. --><!-- A HREF="../../VAST/vast.shtml" --><A HREF="#OriginalVAST"><B>Original VAST</B></A>, which focuses on 3D similarities between individual protein molecules or <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains"><B>3D domains</B></A> (substructures) rather than biological units, is described in the <A HREF="../../VAST/vasthelp.html"><B>original VAST Help document</B></A>. The <A HREF="../../VAST/vast.shtml"><B>VAST Search tool</B></A>, which accepts input of a query structure's 3D coordinates and returns original-style VAST results, is described in the <A HREF="../../VAST/vastsrchelp.html"><B>VAST Search Help document</B></A>.<!-- The "<A HREF="vastplus_how_to.html"><B>How To</B></A>" page provides <A HREF="vast_how_to.html"><B>quick start guides</B></A> that provide some examples of how VAST+ can be used.<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 --></P></TD>
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</TR>
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</TABLE>
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<!-- =========== END_BOXED_SCOPE_NOTE =========== -->
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<!-- ==================== TOC_TABLE_OF_CONTENTS ================= -->
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
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<!-- ================= LEFT_SIDE_TOC ==================== -->
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<TD class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
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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;">DETAILED TABLE OF CONTENTS</TD>
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</TR>
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</TABLE -->
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<A NAME="TOCWhatIs"></A>
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<UL>
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<LI><A HREF="#WhatIs">What is <B>VAST+</B>?</LI>
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<UL>
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||
<LI><!-- A HREF="#VASTplusDefinition" --><A HREF="#WhatIs"><B>V</B>ector <B>A</B>lignment <B>S</B>earch <B>T</B>ool <B><I>Plus</I></B></A></LI>
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<LI><A HREF="#Compare"><span style="color:#d70000">Comparison of original VAST vs. VAST+</span></A></LI>
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<LI><A HREF="#DatabaseApplications"><span style="color:#d70000">How can VAST+ be used to learn more about proteins?</span></A></LI>
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<LI><A HREF="#IllustratedExamples"><span style="color:#d70000">Illustrated examples</span> of VAST+ results for:</A></LI>
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||
<UL>
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||
<LI><A HREF="#IllustratedExample1B26">Glutamate Dehydrogenase (<I>Thermotoga maritima</I><!--, PDB ID 1B26 -->)<!-- (<span style="color:#d70000"><I>illustration</I></span>) --></A></LI>
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||
<LI><A HREF="#IllustratedExample1HBB">Deoxyhemoglobin (<I>Homo sapiens</I><!--, PDB ID 1HBB -->)<!-- (<span style="color:#d70000"><I>illustration</I></span>) --></A></LI>
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||
</UL>
|
||
<LI><A HREF="#PrecalculatedResults">Precalculated results</A></LI>
|
||
</UL>
|
||
</UL>
|
||
|
||
<A NAME="TOCQuickStart"></A>
|
||
<!-- UL>
|
||
<LI><A HREF="#QuickStart"><B>Quick start</B> guide</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#QuickStart">illustrated example showing the <SPAN style="color:#D70000">1-2-3 step process</SPAN> for using the tool</A></LI>
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||
</UL>
|
||
</UL -->
|
||
|
||
<A NAME="TOCInput"></A>
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||
<UL>
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||
<LI><A HREF="#Input"><B>Input Options</B></A></LI>
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||
<UL>
|
||
|
||
<LI><A HREF="#InputID"><B>PDB ID or MMDB ID</B></A></LI>
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||
<UL>
|
||
<LI><A HREF="#InputID">Enter ID directly into search box on <B>VAST Home</B> page</A></LI>
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||
</UL>
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||
|
||
<LI><A HREF="#InputEntrezSearch"><B>Structure or Protein database search</B>:</A><!-- (retrieve records → link to related 3D structures) --></LI>
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||
<UL>
|
||
<LI><A HREF="#InputEntrezStructure2SimilarStructure">3D structure → similar structures<!-- (geometrically similar) --></A></LI>
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||
<LI><A HREF="#InputEntrezProtein2Structure2SimilarStructure">protein sequence → structure<!-- (source structure) -->→ similar structures<!-- (geometrically similar) --></A></LI>
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||
<LI><A HREF="#InputEntrezProtein2RelatedStructure2SimilarStructure">protein sequence → related structures<!-- (sequence-similar) -->→ similar structures<!-- (geometrically similar) --></A></LI>
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||
<!-- UL>
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||
<LI><A HREF="______">__________</A></LI>
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||
<LI><A HREF="______">__________</A></LI>
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||
</UL -->
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||
</UL>
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||
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||
<LI><A HREF="#Input3Dcoordinates"><B>3D coordinates</B></A></LI>
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||
<UL>
|
||
<LI><A HREF="#Input3Dcoordinates">input 3D coordinates of query structure into <B>VAST Search</B> page</A></LI>
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||
</UL>
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||
|
||
</UL>
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||
</UL>
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||
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||
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||
<A NAME="TOCOutput"></A>
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||
<UL>
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||
<LI><A HREF="#Output"><B>Output</B></A></LI>
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||
<UL>
|
||
|
||
<LI><A HREF="#OutputQueryStructure"><B>Query structure (summary information)</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#OutputInteractionsSchematic">Interactions schematic</A></LI>
|
||
<LI><A HREF="#OutputMolecularGraphic">Molecular graphic</A></LI>
|
||
<LI><A HREF="#OutputMMDBID">MMDB ID</A>, <A HREF="#OutputPDBID">PDB ID</A></LI>
|
||
<LI><A HREF="#OutputBiologicalUnit">Biological Unit</A></LI>
|
||
<LI><A HREF="#OutputSourceOrganism">Source Organism</A></LI>
|
||
<LI><A HREF="#OutputNumberOfProteins">Number of proteins</A></LI>
|
||
<LI><A HREF="#OutputNumberOfNucleotides">Number of nucleotides</A></LI>
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||
<LI><A HREF="#OutputNumberOfChemicals">Number of chemicals</A></LI>
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||
</UL>
|
||
|
||
<LI><A HREF="#OutputSimilarStructures"><B>Similar structures</B></A></LI>
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||
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||
<UL>
|
||
<LI><A HREF="#OutputFolderTabs"><B>Folder tabs to select 3D alignment type:</B></A></LI>
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||
<UL>
|
||
<LI><A HREF="#OutputFolderTabInitialAlignment">All matching molecules superposed</A></LI>
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||
<LI><A HREF="#OutputFolderTabRefinedAlignment">Invariant substructure superposed</A></LI>
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||
</UL>
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||
<LI><A HREF="#OutputFilters"><B>Filters to subset the search results<!--Bar Graphs that characterize/filter the search results --> by:</B></A></LI>
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||
<UL>
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||
<LI><A HREF="#OutputFilterMatchedMolecules">Number of aligned protein molecules</A></LI>
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||
<UL>
|
||
<LI><A HREF="#OutputFilterCompleteMatch"><IMG SRC="images/icon_red_circle_solid.png" WIDTH="12" HEIGHT="12" 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 match to biological unit of query structure</A></LI>
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||
<LI><A HREF="#OutputFilterPartialMatch"><IMG SRC="images/icon_red_circle_half_filled.png" WIDTH="12" HEIGHT="12" 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 match to biological unit of query structure</A></LI>
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||
</UL>
|
||
<LI><A HREF="#OutputFilterTaxonomy">Taxonomy</A></LI>
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||
<UL>
|
||
<LI><A HREF="#OutputFilterTaxonomy">Filter results by superkingdom</A></LI>
|
||
</UL>
|
||
</UL>
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||
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||
<LI><A HREF="#OutputRankedList"><B>Ranked list of hits</B></A></LI>
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||
<UL>
|
||
<LI><A HREF="#OutputSortOptions"><B>Sort</B> options</A></LI>
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||
<UL>
|
||
<!-- LI><A HREF="#SortOrder">Default sort order</A></LI -->
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||
<LI><A HREF="#SortOptionAlignedProteins">Aligned proteins</A></LI>
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||
<LI><A HREF="#SortOptionRMSD">RMSD</A></LI>
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||
<LI><A HREF="#SortOptionAlignedResidues">Aligned residues</A></LI>
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||
<LI><A HREF="#SortOptionSequenceIdentity">Sequence identity</A></LI>
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||
<LI><A HREF="#SortOptionTaxonomy">Taxonomy</A></LI>
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||
</UL>
|
||
<LI><A HREF="#OutputViewDetails"><B>View details</B> for a similar structure</A></LI>
|
||
<LI><A HREF="#OutputSearchWithinResults"><B>Search within results</B></A></LI>
|
||
<!-- LI>{<A HREF="#OutputSave"><B>Save</B> search results as CSV file</A>}</LI -->
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||
</UL>
|
||
|
||
</UL>
|
||
|
||
<LI><A HREF="#OutputOriginalVASTButton"><B>"Original VAST" button</B></A></LI>
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||
<UL>
|
||
<LI><A HREF="#OutputOriginalVASTButton">View original style VAST results (by individual protein molecule)</A> <!-- similarities between individual protein molecules or 3D domains --></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#NullResult"><B>"No matched structure found"</B> (null result)</A></LI>
|
||
|
||
<LI><A HREF="#OutputNewSearchButton"><B>"New Search" button</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#OutputNewSearchButton">Enter a new PDB ID or MMDB ID to find similar structures</A></LI>
|
||
</UL>
|
||
|
||
</UL>
|
||
</UL>
|
||
|
||
<A NAME="TOCGraphicalDisplays"></A>
|
||
<UL>
|
||
<LI><A HREF="#GraphicalDisplays"><B>Detailed Views/Graphical Displays for Individual Hits</B></A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#QuerySubjectComparison"><B>Detailed view comparing the query structure and a matched structure</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#AlignedMolecules">Aligned molecules</A></LI>
|
||
<LI><A HREF="#QuerySubjectComparisonInteractionsSchematic">Interaction schematic of query structure vs. matched structure</A></LI>
|
||
<LI><A HREF="#QuerySubjectComparisonProteinList">List of matching protein molecules</A></LI>
|
||
<!-- LI><A HREF="#QuerySubjectComparisonMoleculeGraphic">Matched biological unit [Molecular graphic of subject]</A></LI -->
|
||
</UL>
|
||
|
||
<LI><A HREF="#SeqAlignView"><B>Sequence Alignment Views</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#SeqAlignViewPair">Align one pair of matching molecules</A></LI>
|
||
<LI><A HREF="#SeqAlignViewAll">Display all aligned molecule sequences</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#3DView"><B>3D Views</B></A></LI>
|
||
<UL>
|
||
<!-- LI><A HREF="#3DViewQuery">Query structure 3D view</A></LI -->
|
||
<!-- LI><A HREF="#3DViewSubject">Similar structure (VAST neighbor) 3D view</A></LI -->
|
||
<LI><A HREF="#3DViewSuperposition">Superposition of query and neighbor in 3D</A></LI>
|
||
<!-- UL>
|
||
<LI><A HREF="#3DViewSuperpositionMoleculePair">Superposition of one pair of matching molecules</A></LI>
|
||
<LI><A HREF="#3DViewSuperpositionBiounit">Superposition of biological units</A></LI>
|
||
</UL -->
|
||
<LI><A HREF="#Cn3D">Cn3D version for viewing VAST+ superpositions (important note)</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#OriginalVASTDisplay"><B>Original style VAST display</B> (example)</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#OriginalVASTDisplay"><!-- A HREF="#OriginalVASTDisplayByProteinMolecule" -->similarities between individual protein molecules or 3D domains</A></LI>
|
||
<!-- LI><A HREF="#OriginalVASTDisplayBy3Ddomain">by individual 3D domain</A></LI -->
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
|
||
<A NAME="TOCAlgorithm"></A>
|
||
<UL>
|
||
<LI><A HREF="#Algorithm"><B>VAST+ Algorithm</B></A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#AlgorithmOverview">Overview of method used to identify similarly shaped macromolecular complexes</A></LI>
|
||
|
||
<LI><A HREF="#AlgorithmIllustration"><I><span style="color:#d70000">Illustration</span></I>: VAST+ algorithm</A></LI>
|
||
|
||
<LI><A HREF="#AlgorithmDetails"><I>Additional Details</A></LI>
|
||
|
||
<UL>
|
||
|
||
<!-- LI><A HREF="#AlgorithmMMDBDataProcessing">MMDB Data Processing</A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#AlgorithmGeometricalFeatures">Identifies <B>geometrical features</B> within a structure</A> (<A HREF="#AlgorithmSecondaryStructures"><B>secondary structures</B></A>, <A HREF="#Algorithm3DDomains"><B>3D domains</B></A>)</LI>
|
||
|
||
<LI>[<A HREF="#AlgorithmSecondaryStructures">Identifies <B>secondary structures</B> within a structure</A>]</LI>
|
||
|
||
<LI>[<A HREF="#Algorithm3DDomains">Identifies <B>3D domains</B> within a structure</A>]</LI>
|
||
|
||
<LI><A HREF="#AlgorithmBiologicalUnit">Identifies <B>biological units</B> within a structure</A></LI>
|
||
|
||
</UL>
|
||
|
||
<LI><A HREF="#AlgorithmVAST">Original VAST</A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#AlgorithmIndividualProteins">Compares the shape of <B>individual 3D domains</B> and <B>individual protein molecules</B> throughout the Molecular Modeling Database</A></LI>
|
||
|
||
</UL>
|
||
|
||
|
||
<LI><A HREF="#AlgorithmVASTplus">VAST+</A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#AlgorithmOligomers">Compares the shape of <B>oligomers</B> throughout the Molecular Modeling Database</A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#AlgorithmCompleteMatch">Finds structures that have a <B>complete match</B> to the query structure's biological unit</A></LI>
|
||
|
||
<LI><A HREF="#AlgorithmPartialMatch">Finds structures that have a <B>partial match</B> to the query structure's biological unit</A></LI>
|
||
|
||
</UL>
|
||
|
||
<LI><A HREF="#AlgorithmScore">Calculates <B>scores</B></A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#AlgorithmScoreAlignedProteins">number of <B>aligned proteins</B></A></LI>
|
||
|
||
<LI><A HREF="#AlgorithmScoreRMSD"><B>RMSD</B></A></LI>
|
||
|
||
<LI><A HREF="#AlgorithmScoreAlignedResidues">number of <B>aligned residues</B></A></LI>
|
||
|
||
<LI><A HREF="#AlgorithmScoreSequenceIdentity">percent <B>sequence identity</B></A></LI>
|
||
|
||
</UL -->
|
||
|
||
<LI><A HREF="#AlgorithmAlignment"><!--Generates a --><B>3D alignment</B> of biological units (macromolelcular complexes)</A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#AlgorithmAlignmentInitial"><B>initial alignment</B></A> (all matching molecules superposed)</LI>
|
||
|
||
<LI><A HREF="#AlgorithmAlignmentRefined"><B>refined alignment</B></A> (invariant substructure superposed)</LI>
|
||
|
||
</UL>
|
||
|
||
<!-- /UL -->
|
||
|
||
<LI><A HREF="#AlgorithmSizeLimit"><B>Size limits</B></A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#AlgorithmSizeLimitMinimum"><B>minimum</B> size of structures that are neighbored</A></LI>
|
||
|
||
<LI><A HREF="#AlgorithmSizeLimitMaximum"><B>maximum</B> size of structures that are neighbored</A></LI>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
<A NAME="TOCDefinitions"></A>
|
||
<A NAME="TOCGlossary"></A>
|
||
<!-- UL>
|
||
<LI><A HREF="#Definitions"><A HREF="#Glossary"><B>Glossary</B></A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#Definition%Id">%Id</A></LI>
|
||
|
||
<LI><A HREF="#Definition3DDomain">3D Domain</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionAlignedLength">[<A HREF="#DefinitionAlignmentLength" >]Aligned Length</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionBiologicalUnit">Biological Unit</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionDescription">Description</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionSuperpositionGlobal">Global Superposition</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionGSP">GSP</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionLHM">LHM</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionPVal">P-VAL</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionQuaternaryStructure">Quaternary Structure</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionRelatedStructures">Related Structures</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionRMSD">RMSD</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionScore">Score</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionSimilarStructures">Similar Structures</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionVAST">VAST</A></LI>
|
||
|
||
<LI><A HREF="#DefinitionVASTplus">VAST+</A></LI>
|
||
|
||
<LI><A HREF="#Definition________">________</A></LI>
|
||
|
||
<LI><A HREF="#Definition________">________</A></LI>
|
||
|
||
<LI><A HREF="#Definition________">________</A></LI>
|
||
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
</UL>
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</UL -->
|
||
|
||
|
||
<A NAME="TOCChangeLog"></A>
|
||
<UL>
|
||
<LI><A HREF="#ChangeLog"><B>Log of Changes to VAST+</B></A></LI>
|
||
</UL>
|
||
|
||
<A NAME="TOCReferences"></A>
|
||
<UL>
|
||
<LI><A HREF="#References"><B>References</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#Citing">Citing VAST and VAST+</A></LI>
|
||
<LI><A HREF="#ReferencesAdditional">Additional References</A>
|
||
<!-- LI><A HREF="#ReferencesSupportedDatabases">References describing the supported databases</A></LI -->
|
||
</UL>
|
||
</UL>
|
||
|
||
|
||
<!-- SECTION_HEADER:
|
||
<A NAME="TOC__anchorname___"></A>
|
||
<UL>
|
||
<LI><A HREF="#__anchorname___"><B>_____Section_Header_____</B></A></LI>
|
||
<UL>
|
||
|
||
<LI><A HREF="#________"><B>________</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
</UL>
|
||
</UL>
|
||
|
||
<LI><A HREF="#________"><B>________</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
</UL>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#________">________</A></LI>
|
||
</UL>
|
||
</UL>
|
||
|
||
</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">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell ThumbText2" 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;">BRIEF TABLE OF CONTENTS</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdgeBottomAndSides ThumbText2">
|
||
|
||
<TR>
|
||
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP" colspan="3"> </TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD>
|
||
<TD ALIGN="Left" VALIGN="TOP" style="white-space: nowrap;" class="Yellow1Cell">
|
||
<A HREF="#WhatIs">What is VAST+?</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#VASTplusDefinition">Vector Alignment Search Tool <I>Plus</I></A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#Compare"><span style="color:#d70000">Compare VAST vs. VAST+</span></A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#DatabaseApplications"><span style="color:#d70000">How can VAST+ be used?</span></A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#IllustratedExamples"><span style="color:#d70000"><I>Illustrated examples</I></span> of VAST+ results:</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#IllustratedExample1B26"><!-- span style="color:#d70000"><I>Illustrated example</I></span>: -->Glutamate Dehydrogenase<!-- (<I>Thermotoga maritima</I>, PDB ID 1B26) --></A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#IllustratedExample1HBB"><!-- span style="color:#d70000"><I>Illustrated example</I></span>: -->Deoxyhemoglobin<!-- (<I>Homo sapiens</I>, PDB ID 1HBB) --></A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#PrecalculatedResults">Precalculated results</A><BR>
|
||
|
||
<!-- A HREF="#QuickStart">Quick start guide</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#QuickStartIllustration">1-2-3 step process <I>illustration</I></A><BR -->
|
||
|
||
<A HREF="#Input">Input options</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#InputID">PDB ID or MMDB ID</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#InputEntrezSearch">Structure or Protein database search</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#Input3Dcoordinates">3D coordinates</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#______">___________</A><BR -->
|
||
|
||
<A HREF="#Output">Output</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputQueryStructure">Query structure (summary info)</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputSimilarStructures">Similar structures</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#OutputFolderTabs">Folder tabs to select 3D alignment type</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="80" height="1" border="0"><A HREF="#OutputFolderTabInitialAlignment">all matching molecules superposed</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="80" height="1" border="0"><A HREF="#OutputFolderTabRefinedAlignment">invariant substructure superposed</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#OutputFilters">Filters to subset the search results</A> <A HREF="#OutputFilterCompleteMatch"><IMG SRC="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."></A> <A HREF="#OutputFilterPartialMatch"><IMG SRC="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."></A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#OutputTabularDisplay">Table of similar structures</A><BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#OutputRankedList">Ranked list of hits</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#OutputSortOptions">Sort options</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="80" height="1" border="0"><A HREF="#SortOptionMatchedMolecules">Matched molecules</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="80" height="1" border="0"><A HREF="#SortOptionAlignedProteins">Aligned proteins</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="80" height="1" border="0"><A HREF="#SortOptionRMSD">RMSD</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="80" height="1" border="0"><A HREF="#SortOptionAlignedResidues">Aligned residues</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="80" height="1" border="0"><A HREF="#SortOptionSequenceIdentity">Sequence identity</A><BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#OutputViewDetails">View details for a similar structure</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0"><A HREF="#OutputSearchWithinResults">Search within results</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="60" height="1" border="0">{<A HREF="#OutputSave">Save results as CSV file</A>}<BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputOriginalVAST">"Original VAST" button</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#NullResult">"No matched structure found" (null result)</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputNewSearchButton">"New search" button</A><BR>
|
||
|
||
<A HREF="#GraphicalDisplays">Detailed Views/Graphical Displays</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#QuerySubjectComparison">Query structure vs. matched structure</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SeqAlignView">Sequence Alignment Views</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#3DView">3D Views</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#3DViewSuperposition">3D Structure Superpositions</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OriginalVastDisplay">Original style VAST display</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#______">___________</A><BR -->
|
||
|
||
<A HREF="#Algorithm">VAST+ Algorithm</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmOverview">Overview</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmIllustration"><I><span style="color:#d70000">Illustration: VAST+ algorithm</span></I></A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmDetails">Additional Details</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmSecondaryStructures">Identify secondary structures</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#Algorithm3Ddomains">Identify 3D domains</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmBiologicalUnits">Identify biological units</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmIndividualProteins">Find matches to individual proteins</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmCompleteSimilarity">Find complete matches to biological units</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmPartialSimilarity">Find partial matches to biological units</A><BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmAlignment">3D alignments</A> (<A HREF="#AlgorithmAlignmentInitial">initial</A>, <A HREF="#AlgorithmAlignmentRefined">refined</A>)<BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0">
|
||
<A HREF="#AlgorithmScore">Calculate scores</A><BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0">
|
||
<A HREF="#AlgorithmSizeLimit">Size limits</A>
|
||
(<A HREF="#AlgorithmSizeLimitMinimum">minimum</A>,
|
||
<A HREF="#AlgorithmSizeLimitMaximum">maximum</A>)<BR>
|
||
|
||
<!-- A HREF="#Definitions"><A HREF="#Glossary">Glossary</A><BR -->
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#Input______">____________</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#Input______">____________</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#Input______">____________</A><BR -->
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#______">___________</A><BR -->
|
||
|
||
<A HREF="#ChangeLog">Log of changes to VAST+</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>
|
||
|
||
</TABLE>
|
||
|
||
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR>
|
||
<BR>
|
||
|
||
<!-- ======= SINGLE_THUMBNAIL_YELLOW_BACKGROUND_BIOSYSTEM_RECORD ========== -->
|
||
|
||
<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell ThumbText2" 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">BIOSYSTEM RECORD COMPONENTS & FEATURES</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="#SummaryPage"><IMG src="images/bsid82991_biosystem_record_thumbnail_callouts.png" width="280" height="500" border=0 align="center" alt="Thumbnail image showing portions of the NCBI BioSystems record bsid82991, for human arachidonic acid. Click on image to read more about biosystem record components and features in this help document."></A>
|
||
</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_HIGHLIGHT_COMPONENTS ======== -->
|
||
|
||
<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell ThumbText2" 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="#BSSummaryHighightSelected">HIGHLIGHT SELECTED BIOSYSTEM COMPONENTS</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>
|
||
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|
||
<A HREF="#BSSummaryHighightSelected"><IMG src="images/bsid82991_ptgs1_highlighted_thumbnail.png" width="280" height="270" border=0 align="center" alt="Thumbnail image illustrating the highlight function. In this example, the PTGS1 gene, a component of the arachidonic acid metabolism pathway, is selected in the Genes folder tab of NCBI BioSystems record bsid82991 and then shown with a red outline in the full size image of that pathway on the web server of the source database, KEGG. Click on the image to read more about highlighting selected biosystem components."></A>
|
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||
<!-- BR><BR>
|
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<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>
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||
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||
|
||
<BR><BR><BR>
|
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<A HREF="#______">Thumbnail header/key concept</A><br>
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<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>
|
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||
|
||
<BR><BR><BR>
|
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<A HREF="#______">Thumbnail header/key concept</A><br>
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<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>
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||
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||
|
||
<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>
|
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<BR><BR -->
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||
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<!-- ############ END_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT_AND_TOC ######## -->
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<!-- ==================== VERTICAL SPACER ======================= -->
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<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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||
<TD class="WhiteCell NormalText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
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<!-- ================== END_VERTICAL SPACER ===================== -->
|
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||
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||
<!-- ########### BLUE_HEADER_SECTION_1_WHAT_IS_VASTplus ############# -->
|
||
|
||
<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 is VAST+ ?</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>
|
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</TR>
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||
</TABLE>
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<!-- ############## END_BLUE_HEADER_SECTION_1_WHAT_IS_VASTplus ############ -->
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<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ########### -->
|
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<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
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<TD class="WhiteCellBlueEdgeAll">
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|
||
<!-- ============ MINI_TOC_FOR_THIS_SECTION ============== -->
|
||
<BR>
|
||
<BLOCKQUOTE>
|
||
|
||
<A HREF="#VASTplusDefinition">definition</A> | <A HREF="#Compare">comparison of original VAST vs. VAST+</A> | <A HREF="#DatabaseApplications"><span style="color:#d70000">how can VAST+ be used to learn more about proteins</span></A> | <A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span> of VAST+ results for:</A> <A HREF="#IllustratedExample1B26">glutamate dehydrogenase</A>, <A HREF="#IllustratedExample1HBB">deoxyhemoglobin</A> | <A HREF="#PrecalculatedResults">precalculated results</A>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
||
|
||
<!-- ================= LEVEL_1_VASTplus_DEFINITION ==================== -->
|
||
|
||
<A NAME="VASTplusDefinition"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>VAST+ (Vector Alignment Search Tool <I>Plus</I>) Definition</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 HREF="../vastplus.cgi"><B>VAST+</B></A> is a tool designed to compare 3-dimensional structures, with an emphasis on finding those with <B>similar macromolecular complexes</B>. The similarities are calculated using purely geometric criteria, without regard to sequence similarity, and therefore can identify distant homologs.<!--The similarities are calculated using purely geometric criteria, and therefore can identify distant homologs that cannot be recognized by sequence comparison. --><BR><BR>
|
||
|
||
VAST+ is built upon the original <A HREF="../../VAST/vast.shtml">Vector Alignment Search Tool (<B>VAST</B>)</A>, and expands the capabilities of that program by making it possible to now find macromolecular structures that have similarly shaped <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological units</A> (also referred to as "biounits"), not just those that share similarly shaped individual protein molecules or fragments.<BR><BR>
|
||
|
||
The <B>similar structures</B> found by the programs are often referred to as "<B>neighbors</B>." <B>VAST neighbors</B> are structures that contain similarly shaped individual protein molecules or <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domains</A>, and <B>VAST+ neighbors</B> are structures that have similarly shaped <A HREF="#OutputBiologicalUnit">biological units</A>.<BR>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- =============== END_LEVEL_1_VASTplus_DEFINITION ================== -->
|
||
|
||
<!-- ============== LEVEL_1_COMPARE_VAST_vs_VAST+ ============= -->
|
||
|
||
<A NAME="Compare"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Comparison of original <A HREF="../../VAST/vast.shtml"><B>VAST</B></A> vs. <A HREF="../vastplus.cgi"><B>VAST+</B></A></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="CompareOriginalVAST"></A>The <B>original</B> <A HREF="../../VAST/vast.shtml"><B>VAST</B></A> identifies <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domains</A> (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other protein structures that have one or more similar 3D domains, using purely geometric criteria. The original VAST output <!-- I>(<A HREF="#OriginalVASTDisplay"><span style="color:#d70000">{illustrated example}</span></A>)</I --> reflects <!-- is based on, displays, reflects, emphasizes -->comparisons between <B>individual protein molecules</B>, which can share a similar shape along their entire length, or only along a fraction of their length, such as a <B>single 3D domain</B><!-- [The VAST output is based on comparisons between individual protein molecules from a query structure and a hit, where the proteins can share a similar shape along their entire length, or only along a fraction of their length. In this way, original VAST provides an emphasis on <A HREF="../../MMDB/docs/mmdb_help.html#FourLevelsOfStructure">tertiary structure</A> of proteins.] --> <!-- I>(The <A HREF="../../MMDB/docs/mmdb_help.html">MMMDB help document</A> provides details about <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">[<A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvProteins3dDomains">]3D domains</A> and the <A HREF="../../MMDB/docs/mmdb_help.html#FourLevelsOfStructure">four levels of protein structure</A>.)</I --> <I>(<A HREF="#OriginalVASTDisplay"><span style="color:#d70000">illustrated example of original VAST results</span></A>)</I>. That output is available by clicking the "Original VAST" button near the upper right hand corner of a VAST+ results page. Additionally, that output is shown by default if you enter a query on the <A HREF="../../VAST/vast.shtml">Original VAST home page</A>, or if a particular query structure <A HREF="#NullResult">does not have any VAST+ neighbors but does have original VAST neighbors</A>.<BR><BR>
|
||
|
||
<A NAME="CompareVASTplus"></A><A HREF="../vastplus.cgi"><B>VAST+</B></A>, on the other hand, focuses primarily on finding other macromolecular structures that have a similar <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A><!-- I>(<A HREF="#RankedListIllustration"><span style="color:#d70000">{illustrated example}</span></A>)</I -->, rather than those that are similar at the level of an individual protein molecule or <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domain</A> <I>(<A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples of VAST+ results</span></A>)</I>. To do this, VAST+ takes into consideration the complete set of 3D domains that VAST identified within a query structure, throughout all of its component protein molecules, and finds other macromolecular structures that have a similar set of proteins/3D domains. In this way, it is an <B>extension of the original VAST</B>, and reveals <B>macromolecular complexes</B> that are similar to each other by taking their <A HREF="../../MMDB/docs/mmdb_help.html#FourLevelsOfStructure">quaternary structure</A> into account.<!-- (The MMMDB help document provides details about the <A HREF="../../MMDB/docs/mmdb_help.html#FourLevelsOfStructure">four levels of protein structure</A>.) --> VAST+ <A HREF="#Output">output</A> ranks the similar structures based on the extent of their similarity to the query structure, first listing <A HREF="#OutputFilterCompleteMatch"><IMG SRC="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="#OutputFilterPartialMatch"><IMG SRC="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. Matches to individual 3D domains within protein molecules are not displayed in VAST+, but are still accessible by following the "<A HREF="#OutputOriginalVAST">Original VAST</A>" link that is provided on a VAST+ results page.<BR><BR><BR>
|
||
|
||
<!-- ============ COMPARE_TABLE_ORIGNAL_VAST_VS_VAST+ ============ -->
|
||
|
||
<A NAME="CompareTable"></A>
|
||
<TABLE style="margin:0px 0px 0px 0px;" cellpadding="4" class="format1 NormalText">
|
||
|
||
<TR>
|
||
<TD width="50%" class="format1H" style="white-space: nowrap;">Use <A HREF="../../VAST/vast.shtml"><B>Original VAST</B></A> if you want to:</TD>
|
||
<TD width="50%" class="format1H" ALIGN="LEFT">Use <A HREF="../vastplus.cgi"><B>VAST+</B></A> if you want to:</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top"><UL><LI>Focus on 3-dimensional similarities between <B>individual protein molecules</B>, or between <B>individual</B> <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains"><B>3D domains</B></A>.<BR><I>(Original VAST lists each protein molecule and 3D domain in the <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A> of the query structure, and links to structures that are similar in shape to the protein molecule or 3D domain you select.)</I><BR><I><A HREF="#OriginalVASTDisplay"><span style="color:#d70000">illustrated example...</span></A></I></LI></UL></TD>
|
||
<TD class="format1B" valign="top"><UL><LI>Focus on 3-dimensional similarities between <B>macromolecular complexes</B> (<!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological units</A>).<BR><I><A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples...</span></A></I></LI></UL></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top"><UL><LI>View the superposition of <B>two *or more*</B> <B>protein molecules</B> at the same time.</LI></UL></TD>
|
||
<TD class="format1B" valign="top"><UL><LI>View the superposition of <B>two</B> <B>macromolecular complexes</B><BR>
|
||
<I>(The latest version of NCBI's structure viewing program, <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> 4.3.1, is needed in order to do this.)</I></LI></UL></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top"><UL><LI>Align (in 3D space) two or more proteins from the <B>same structure record</B>.</LI></UL></TD>
|
||
<TD class="format1B" valign="top"><UL><LI><B>Rank structures</B> by their degree of similarity to the query protein's <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A>.</LI></UL></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top"><UL><LI>Align (in 3D space) two or more domains from the <B>same molecule</B> to each other, for example, to compare repeats.<BR>
|
||
<I>(For example, compare the first and second immunoglobulin (Ig) domain in a protein molecule.)</I></LI></UL></TD>
|
||
<TD class="format1B" valign="top"><UL><LI>Compare <B>different states of the same oligomer</B>. <I>(For example, compare the conformation of the deoxygenated and oxygenated states of hemoglobin.)</I></LI></UL></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top"><img SRC="/Structure/IMG/spacer.gif" width="30" height="15" border="0"><A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB&style=old"><B>Live example</B> of original VAST results for<BR>
|
||
<img SRC="/Structure/IMG/spacer.gif" width="30" height="1" border="0"><B>1HBB</B>, deoxyhemoglobin (<I>Homo sapiens</I>)</A>.<BR><BR></TD>
|
||
<TD class="format1B" valign="top"><img SRC="/Structure/IMG/spacer.gif" width="30" height="15" border="0"><A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB "><B>Live example</B> of VAST+ results for<BR>
|
||
<img SRC="/Structure/IMG/spacer.gif" width="30" height="1" border="0"><B>1HBB</B>, deoxyhemoglobin (<I>Homo sapiens</I>)</A>.<BR><BR></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD class="format1A" valign="top"><img SRC="/Structure/IMG/spacer.gif" width="30" height="15" border="0"><A HREF="#OriginalVASTDisplay"><B>Illustrated/annotated example</B> of original VAST results<BR>
|
||
<img SRC="/Structure/IMG/spacer.gif" width="30" height="1" border="0">for <B>1PTH</B>, prostaglandin H2 synthase-1 (<I>Ovis aries</I>)</A>.<BR><BR></TD>
|
||
<TD class="format1B" valign="top"><img SRC="/Structure/IMG/spacer.gif" width="30" height="15" border="0"><A HREF="#IllustratedExamples"><B>Illustrated/annotated examples</B> of VAST+ results for</A><BR>
|
||
<img SRC="/Structure/IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#IllustratedExample1B26"><B>1B26</B>, glutamate dehydrogenase (<I>Thermotoga maritima</I>)</A>, and<BR>
|
||
<img SRC="/Structure/IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#IllustratedExample1HBB"><B>1HBB</B>, deoxyhemoglobin (<I>Homo sapiens</I>)</A>.<BR><BR></TD>
|
||
</TR>
|
||
|
||
<!-- indented text in column 1 and 2 with up arrow in column 2 -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top">
|
||
<P class="indent20">____col_1_indented__</P></TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><IMG SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></IMG></A>
|
||
<P class="indent20">____________col_2_indented_________</P></TD>
|
||
</TR -->
|
||
|
||
<!-- to use image for indentation rather than paragraph style: -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top"><img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0">____col_1_indented__</TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><IMG SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></IMG></A>
|
||
<img SRC="/Structure/IMG/spacer.gif" width="25" height="1" border="0">____________col_2_indented_________</TD>
|
||
</TR -->
|
||
|
||
<!-- template for table row WITHOUT bullet and WITH up arrow -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top">____col_1___</TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><IMG SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></IMG></A>
|
||
____________col_2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- template for table row WITH bullet and WITHOUT up arrow -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1A" valign="top"><UL><LI>____col_1___</LI></UL></TD>
|
||
<TD class="format1B" valign="top"><UL><LI>____col_2___</LI></UL></TD>
|
||
</TR -->
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- ============ END_COMPARE_TABLE_ORIGNAL_VAST_VS_VAST+ ============ -->
|
||
|
||
<!-- ============ COMPARE_LINKS_ORIGNAL_VAST_VS_VAST+ ============ -->
|
||
|
||
<!-- To compare the views directly, you can:<BR>
|
||
|
||
- <A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB ">open a live web page with <B>VAST+ results</B> for 1HBB</A><BR>
|
||
|
||
- <A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB&style=old">open a live web page with <B>original-style VAST results</B> for 1HBB</A><BR>
|
||
|
||
[-<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113&ShowOp=VastSum">open a live web page with <B>original-style VAST results</B> for 1HBB</A><BR>]
|
||
|
||
<I>(Tip: Right click on each link above and select "open in new window" in order to be able to compare the views side by side. This help document explains the features and functions of the [<A HREF="../vastplus/vastplus.cgi">]VAST+ results page, and the <A HREF="../../VAST/vasthelp.html">original VAST help document</A> explains the features and functions of the original VAST results page.)</I><BR><BR><BR -->
|
||
|
||
<!-- ============ END_COMPARE_LINKS_ORIGNAL_VAST_VS_VAST+ ============ -->
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============== END_LEVEL_1_COMPARE_VAST_vs_VAST+ ============= -->
|
||
|
||
<!-- ============== LEVEL_1_VASTplus_USEFUL_FEATURES ============= -->
|
||
|
||
<A NAME="DatabaseApplications"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>How can VAST+ be used to learn more about proteins?</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>
|
||
Because <A HREF="../vastplus.cgi">VAST+</A> emphasizes the identification of similar <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological units</A>, it is now possible to:
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="ExampleSameOligomer"></A>Find protein complexes that have the <B>same oligomeric state and similarly shaped proteins</B>, regardless of the degree of sequence similarity.<!-- Find structures that have similarly shaped proteins and the same oligomeric state, regardless of degree of sequence similarity. --></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>Example: view the <A HREF="/Structure/vastplus/vastplus.cgi?uid=4MGG"><B>VAST+ neighbors for 4MGG</B></A>: Crystal Structure of an Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata IAM 12614 (Target Nysgrc-012903) With Bound MG, Space Group P212121.<BR>
|
||
<I>(Included among the VAST+ results are structures such as <A HREF="/Structure/vastplus/vastplus.cgi?uid=4mgg&find=3sn4"><B>3SN4</B></A>, which has remarkable conservation of the overall complex structure, despite very low sequence similarity.)</I></LI><BR>
|
||
|
||
<!-- LI>Example: view the <A HREF="/Structure/vastplus/vastplus.cgi?uid=4MGG"><B>VAST+ neighbors</B></A> for query structure <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=113963">4MGG</A>: Crystal Structure of an Enolase (Mandelate Racemase Subgroup) From Labrenzia Aggregata IAM 12614 (Target Nysgrc-012903) With Bound MG, Space Group P212121.</LI -->
|
||
|
||
<LI>Example: view the <A HREF="/Structure/vastplus/vastplus.cgi?uid=1B26"><B>VAST+ neighbors for 1B26</B></A>: Crystal structure of glutamate dehydrogenase from the hyperthermophilic eubacterium thermotoga maritima at 3.0 Å resolution.<BR>
|
||
<I>(Included among the VAST+ results are structures such as <A HREF="/Structure/vastplus/vastplus.cgi?uid=1b26&find=1gtm"><B>1GTM</B></A>, which has a similarly shaped proteins and a hexameric <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A>, but a somewhat different configuation of the hexamer when compared with the query structure, as shown in the <A HREF="#IllustratedExample1B26">illustrated example</A> below.)</I></LI>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="ExampleSameOligomerDifferentState"></A>Compare the conformation of <B>different states of the same oligomer</B>, such as oxy- and deoxyhemoglobin.</LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>Example: view the <A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB"><B>VAST+ neighbors for 1HBB</B></A>: High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site.<BR>
|
||
<I>(Included among the VAST+ results are structures such as <A HREF="/Structure/vastplus/vastplus.cgi?uid=1hbb&find=1gzx"><B>1GZX</B></A>, an oxy T State hemoglobin, which can be viewed as a 3D superposition on the query structure, to compare configurations, using <!-- A HREF="../../CN3D/cn3d.shtml" --><A HREF="#Cn3D">Cn3D 4.3.1</A>.)</I></LI>
|
||
|
||
<!-- LI>Example: view the <A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB"><B>VAST+ neighbors</B></A> for query structure <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113">1HBB</A>: High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site.</LI -->
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
|
||
<LI><A NAME="ExampleBindingInterface"></A>Compare the <B>binding interfaces</B> of a query structure and its nearest "neighbors," such as the differences in the binding interface among similarly shaped immunocomplexes<!-- such as differences in the MHC binding interface with variants of the T-cell receptor -->.</LI><BR>
|
||
<UL>
|
||
<LI>Example: view the <A HREF="/Structure/vastplus/vastplus.cgi?uid=3O6F"><B>VAST+ neighbors for 3O6F</B></A>: Crystal Structure of a Human Autoimmune TCR Ms2-3c8 Bound to MHC Class II Self-ligand Mbphla-dr4.<BR>
|
||
<I>(Included among the VAST+ results are structures such as <A HREF="/Structure/vastplus/vastplus.cgi?uid=3o6f&find=1j8h"><B>1J8H</B></A>, which contains a complex between HLA-DR3, an Influenza hemagglutinin peptide, and a human alpha/beta T-cell receptor. This demonstrates how well the auto-reactive T-cell receptor complex mimics complexes that include foreign peptides.)</I></LI>
|
||
|
||
<!-- LI>Example: view the <A HREF="/Structure/vastplus/vastplus.cgi?uid=3O6F"><B>VAST+ neighbors</B></A> for query structure <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=88951">3O6F</A>: Crystal Structure of a Human Autoimmune TCR Ms2-3c8 Bound to MHC Class II Self-ligand Mbphla-dr4.</LI -->
|
||
</UL>
|
||
<BR>
|
||
|
||
<!-- UL>
|
||
<LI><P class="pad10">_______________________</P></LI>
|
||
<LI><P class="pad10">_______________________</P></LI>
|
||
<LI><P class="pad10">_______________________</P></LI>
|
||
</UL -->
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============== END_LEVEL_1_VASTplus_USEFUL_FEATURES ============= -->
|
||
|
||
<A NAME="IllustratedExamples"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Illustrated examples of VAST+ 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>
|
||
|
||
<!-- ============ MINI_TOC_FOR_THIS_SECTION ============== -->
|
||
<BLOCKQUOTE>
|
||
<A HREF="#IllustratedExample1B26">glutamate dehydrogenase (<I>Thermotoga maritima</I>)</A> | <A HREF="#IllustratedExample1HBB">deoxyhemoglobin (<I>Homo sapiens</I>)</A>
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
||
|
||
<!-- ============== LEVEL_1_ILLUSTRATED_EXAMPLE_1B26 ============= -->
|
||
|
||
<A NAME="IllustratedExample1B26"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Illustrated Example:  VAST+ results for Glutamate Dehydrogenase (<I>Thermotoga maritima</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>
|
||
<BR>
|
||
|
||
<!--BLOCKQUOTE -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
|
||
|
||
<TR>
|
||
|
||
<TD class="WhiteCell" WIDTH="30" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
|
||
<TD class="WhiteCell" ALIGN="Left" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="5" class="WhiteCell NormalText3">
|
||
|
||
<TR>
|
||
<TD class="Yellow1CellBlueEdge" ALIGN="Center" VALIGN="Top" COLSPAN="3">
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="5" border="0">
|
||
<P class="indent20bottomspace NormalText3"><B>VAST+ search results<!-- ,<BR>
|
||
with detailed query vs. subject comparison --> for <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=11869">1B26</A> Glutamate Dehydrogenase (<I>Thermotoga maritima</I>)</B>,<BR>
|
||
as of 02 October 2014, with detailed view of match to <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=5314">1GTM</A><!-- Structure of Glutamate Dehydrogenase (<I>Pyrococcus furiosus</I>) -->. Click anywhere on the image to<BR><A HREF="/Structure/vastplus/vastplus.cgi?uid=1B26">open a live web page with current VAST+ results for 1B26</A>.</P>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="5" border="0">
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- to hide the column on the right with links to more info about each element of the VAST+ search results page, (1) use the TR below, (2) set the width of this immediate table to 550; and (3) set colspan for title cell to colspan1 -->
|
||
|
||
<!--TR>
|
||
<TD WIDTH="540" class="WhiteCellBlueEdgeBottomAndSides" ALIGN="Center" VALIGN="TOP">
|
||
<A HREF="/Structure/vastplus/vastplus.cgi?uid=1B26"><IMG SRC="images/1B26_vastplus_neighbor_1GTM.png" WIDTH="530" HEIGHT="645" BORDER="0" ALT="Detailed comparison of a query structure and a VAST+ similar structure, listing names of aligned molecules and alignment statistics, for the alignment of 1B26 (Glutamate Dehydrogenase from Thermotoga maritima) and 1GTM (Glutamate Dehydrogenase from Pyrococcus furiosus). Click on the image to open a live web page with VAST+ results for 1B26."></A><BR><BR>
|
||
<A HREF="/Structure/vastplus/vastplus.cgi?uid=1B26 ">Open a live web page with current VAST+ results for 1B26</A></TD>
|
||
</TR -->
|
||
|
||
<!-- to reveal the column on the right with links to more info about each element of the VAST+ search results page, (1) use the TR below, (2) set the width of this immediate table to 100%; and (3) set colspan for title cell to colspan3 -->
|
||
|
||
<TR>
|
||
<TD WIDTH="530" class="WhiteCellBlueEdgeBottomAndLeft" ALIGN="Center" VALIGN="TOP">
|
||
<A HREF="/Structure/vastplus/vastplus.cgi?uid=1B26"><IMG SRC="images/1B26_vastplus_neighbor_1GTM.png" WIDTH="530" HEIGHT="645" BORDER="0" ALT="Detailed comparison of a query structure and a VAST+ similar structure, listing names of aligned molecules and alignment statistics, for the alignment of 1B26 (Glutamate Dehydrogenase from Thermotoga maritima) and 1GTM (Glutamate Dehydrogenase from Pyrococcus furiosus). Click on the image to open a live web page with VAST+ results for 1B26."></A><BR><BR>
|
||
<A HREF="/Structure/vastplus/vastplus.cgi?uid=1B26 ">Open a live web page with current VAST+ results for 1B26</A></TD>
|
||
<TD class="Yellow1CellBlueEdgeBottomAndLeft" WIDTH="5" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
<TD class="Yellow1CellBlueEdgeBottomAndRight" WIDTH="215" ALIGN="Left" VALIGN="TOP" style="white-space: nowrap;">Read more about:<BR><BR>
|
||
|
||
<A HREF="#Input">Input options</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#InputID">PDB ID or MMDB ID</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#InputEntrezSearch">Structure or Protein database search</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#Input3Dcoordinates">3D coordinates</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#______">___________</A><BR --><BR>
|
||
|
||
<A HREF="#Output">Output</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OutputQueryStructure">Query structure (summary info):</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputInteractionsSchematic">interactions schematic</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputMolecularGraphic">molecular graphic</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputMMDBID">MMDB ID</A>, <A HREF="#OutputPDBID">PDB ID</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputBiologicalUnit">biological unit</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputSourceOrganism">source organism</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputNumberOfProteins">number of proteins</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputNumberOfNucleotides">number of nucleotides</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputNumberOfChemicals">number of chemicals</A><BR><BR>
|
||
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OutputSimilarStructures">Similar structures</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputFolderTabs">Folder tabs to select 3D alignment type</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputFolderTabInitialAlignment">all matching molecules superposed</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputFolderTabRefinedAlignment">invariant substructure superposed</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputFilters">Filters to subset the search results</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="12" border="0"><A HREF="#OutputFilterCompleteMatch"><IMG SRC="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 biounit matches</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="12" border="0"><A HREF="#OutputFilterPartialMatch"><IMG SRC="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 biounit matches</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="50" height="12" border="0"><A HREF="#OutputFilterTaxonomy">taxonomy</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputTabularDisplay">Table of similar structures</A><BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputRankedList">Ranked list of hits</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputSortOptions">Sort options</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionMatchedMolecules">Matched molecules</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionAlignedProteins">Aligned proteins</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionRMSD">RMSD</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionAlignedResidues">Aligned residues</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionSequenceIdentity">Sequence identity</A><BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputViewDetails">View details for a similar structure</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputSearchWithinResults">Search within results</A><BR><BR>
|
||
|
||
<!-- img SRC="../../IMG/spacer.gif" width="30" height="1" border="0">{<A HREF="#OutputSave">Save results as CSV file</A>}<BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OutputOriginalVAST">"Original VAST" button</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#NullResult">"No matched structure found"<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0">(null result)</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OutputNewSearchButton">"New search" button</A><BR><BR>
|
||
|
||
<A HREF="#GraphicalDisplays">Detailed Views/Graphical Displays</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#QuerySubjectComparison">Query Structure vs. Matched Structure</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#SeqAlignView">Sequence Alignment Views</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#3DView">3D Views</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#3DViewSuperposition">3D Structure Superpositions</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OriginalVastDisplay">Original style VAST display</A><BR>
|
||
|
||
</TD>
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</TD>
|
||
|
||
<TD class="WhiteCell" WIDTH="20" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<!-- /BLOCKQUOTE -->
|
||
<BR><BR>
|
||
|
||
<!-- ============= END_LEVEL_1_ILLUSTRATED_EXAMPLE_1B26 ========== -->
|
||
|
||
<!-- ============== LEVEL_1_ILLUSTRATED_EXAMPLE_1HBB ============= -->
|
||
|
||
<A NAME="IllustratedExample1HBB"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Illustrated Example:  VAST+ results for Deoxyhemoglobin (<I>Homo sapiens</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>
|
||
<BR>
|
||
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
|
||
|
||
<TR>
|
||
|
||
<TD class="WhiteCell" WIDTH="30" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
|
||
<TD class="WhiteCell" ALIGN="Left" VALIGN="TOP">
|
||
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="5" class="WhiteCell NormalText3">
|
||
|
||
<TR>
|
||
<TD class="Yellow1CellBlueEdge" ALIGN="Center" VALIGN="Top" COLSPAN="3">
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="5" border="0">
|
||
<P class="indent20bottomspace NormalText3">
|
||
<B>VAST+ search results for <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113">1HBB</A> High-resolution X-ray Study of Deoxyhemoglobin<BR>Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site</B>,<BR>
|
||
as of 02 October 2014, with detailed view of match to <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=4611">1FSL</A><!--, Ferric Soybean Leghemoglobin Complexed With Nicotinate -->. Click anywhere on the image to<BR><A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB">open a live web page with current VAST+ results for 1HBB</A>.</P>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="5" border="0">
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- to hide the column on the right with links to more info about each element of the VAST+ search results page, (1) use the TR below, (2) set the width of this immediate table to 550; and (3) set colspan for title cell to colspan1 -->
|
||
|
||
<!--TR>
|
||
<TD WIDTH="540" class="WhiteCellBlueEdgeBottomAndSides" ALIGN="Center" VALIGN="TOP">
|
||
<A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB"><IMG SRC="images/1HBB_vastplus_neighbors.png" WIDTH="530" HEIGHT="1350" BORDER="0" ALT="Illustrated example of VAST+ search results for 1HBB (High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site) and 1FSL (Ferric Soybean Leghemoglobin Complexed With Nicotinate), showing a detailed comparison of the query structure and a VAST+ similar structure, listing names of aligned molecules and alignment statistics, for the alignment. Click on the image to open a live web page with VAST+ results for 1HBB."></A><BR><BR>
|
||
<A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB">Open a live web page with current VAST+ results for 1HBB</A></TD>
|
||
</TR -->
|
||
|
||
<!-- to reveal the column on the right with links to more info about each element of the VAST+ search results page, (1) use the TR below, (2) set the width of this immediate table to 100%; and (3) set colspan for title cell to colspan3 -->
|
||
|
||
<TR>
|
||
<TD WIDTH="530" class="WhiteCellBlueEdgeBottomAndLeft" ALIGN="Center" VALIGN="TOP">
|
||
<A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB"><IMG SRC="images/1HBB_vastplus_neighbors.png" WIDTH="530" HEIGHT="1350" BORDER="0" ALT="Illustrated example of VAST+ search results for 1HBB (High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site) and 1FSL (Ferric Soybean Leghemoglobin Complexed With Nicotinate), showing a detailed comparison of the query structure and a VAST+ similar structure, listing names of aligned molecules and alignment statistics, for the alignment. Click on the image to open a live web page with VAST+ results for 1HBB."></A><BR><BR>
|
||
<A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB">Open a live web page with current VAST+ results for 1HBB</A></TD>
|
||
<TD class="Yellow1CellBlueEdgeBottomAndLeft" WIDTH="10" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
<TD class="Yellow1CellBlueEdgeBottomAndRight" WIDTH="200" ALIGN="Left" VALIGN="TOP" style="white-space: nowrap;">Read more about:<BR><BR>
|
||
|
||
<A HREF="#Input">Input options</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#InputID">PDB ID or MMDB ID</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#InputEntrezSearch">Structure or Protein database search</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#Input3Dcoordinates">3D coordinates</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#______">___________</A><BR --><BR>
|
||
|
||
<A HREF="#Output">Output</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OutputQueryStructure">Query structure (summary info):</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputInteractionsSchematic">interactions schematic</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputMolecularGraphic">molecular graphic</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputMMDBID">MMDB ID</A>, <A HREF="#OutputPDBID">PDB ID</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputBiologicalUnit">biological unit</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputSourceOrganism">source organism</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputNumberOfProteins">number of proteins</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputNumberOfNucleotides">number of nucleotides</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputNumberOfChemicals">number of chemicals</A><BR><BR>
|
||
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OutputSimilarStructures">Similar structures</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputFolderTabs">Folder tabs to select 3D alignment type</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputFolderTabInitialAlignment">all matching molecules superposed</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputFolderTabRefinedAlignment">invariant substructure superposed</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputFilters">Filters to subset the search results</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="12" border="0"><A HREF="#OutputFilterCompleteMatch"><IMG SRC="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."> full biounit matches</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="12" border="0"><A HREF="#OutputFilterPartialMatch"><IMG SRC="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 biounit matches</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="50" height="12" border="0"><A HREF="#OutputFilterTaxonomy">taxonomy</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputTabularDisplay">Table of similar structures</A><BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputRankedList">Ranked list of hits</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputSortOptions">Sort options</A><BR>
|
||
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionMatchedMolecules">Matched molecules</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionAlignedProteins">Aligned proteins</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionRMSD">RMSD</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionAlignedResidues">Aligned residues</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SortOptionSequenceIdentity">Sequence identity</A><BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputViewDetails">View details for a similar structure</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0"><A HREF="#OutputSearchWithinResults">Search within results</A><BR><BR>
|
||
|
||
<!-- img SRC="../../IMG/spacer.gif" width="30" height="1" border="0">{<A HREF="#OutputSave">Save results as CSV file</A>}<BR -->
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OutputOriginalVAST">"Original VAST" button</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#NullResult">"No matched structure found"<BR>
|
||
<img SRC="../../IMG/spacer.gif" width="30" height="1" border="0">(null result)</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OutputNewSearchButton">"New search" button</A><BR><BR>
|
||
|
||
<A HREF="#GraphicalDisplays">Detailed Views/Graphical Displays</A><BR><BR>
|
||
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#QuerySubjectComparison">Query Structure vs. Matched Structure</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#SeqAlignView">Sequence Alignment Views</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#3DView">3D Views</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#3DViewSuperposition">3D Structure Superpositions</A><BR>
|
||
<img SRC="../../IMG/spacer.gif" width="15" height="1" border="0"><A HREF="#OriginalVastDisplay">Original style VAST display</A><BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</TD>
|
||
|
||
<TD class="WhiteCell" WIDTH="20" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
<BR><BR>
|
||
|
||
<!-- ============== END_LEVEL_1_ILLUSTRATED_EXAMPLE_1HBB ============= -->
|
||
|
||
<!-- ============== LEVEL_1_VASTplus_precalculated_neighbors ============= -->
|
||
|
||
<A NAME="PrecalculatedResults"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>VAST+ results are precalculated for structures in MMDB</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>
|
||
|
||
VAST+ results are precalculated for structures that are publicly available in the <A HREF="/structure"><B>Molecular Modeling Database (MMDB)</B></A>, as part of the <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingRelatedStructures">MMDB data processing</A> pipeline, and the results are updated each week as new structures are added to the database.<!-- The <B>similar structures</B> are often referred to as "<B>neighbors</B>." --><BR><BR>
|
||
|
||
To see the VAST+ neighbors for a structure of interest, you can either <A HREF="#Input">input</A> the (a) <A HREF="#InputID">PDB ID or MMDB ID</A> for the query structure on the <A HREF="../vastplus.cgi">VAST+</A> home page, or (b) start with a <A HREF="#InputEntrezSearch">Structure or Protein database search</A> and then follow links for "similar structures." In either case, VAST+ <A HREF="#Output">output</A> will display a list of similar structures, ranking them by the extent of their similarity to the query structure's <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A>.<BR><BR>
|
||
|
||
<I>If your query structure is not yet available in MMDB, then you can <A HREF="#Input3Dcoordinates">input your structure's 3D coordinates</A> into the <A HREF="/Structure/VAST/vastsearch.html ">VAST Search </A> program, which will find 3D similar structures and display them in the <A HREF="#OutputOriginalVAST">original VAST output</A> format.</I><BR>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- =========== END_LEVEL_1_VASTplus_precalculated_neighbors ========== -->
|
||
|
||
<!-- ====== 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 ===================== -->
|
||
|
||
<!-- ########### BLUE_HEADER_SECTION_2_QUICK_START ############# -->
|
||
|
||
<A NAME="QuickStart"></A>
|
||
|
||
<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Quick Start Guide</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_QUICK_START ############ -->
|
||
|
||
|
||
<!-- ########## 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" -->
|
||
|
||
<!-- ============ MINI_TOC_FOR_THIS_SECTION ============== -->
|
||
<!-- BR>
|
||
<BLOCKQUOTE>
|
||
|
||
<A HREF="#_____">_________</A> | <A HREF="#_____">_________</A> | <A HREF="#_____">_________</A> | <A HREF="#_____">_________</A>
|
||
|
||
</BLOCKQUOTE -->
|
||
|
||
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
||
|
||
<!-- ================= LEVEL_1 ==================== -->
|
||
|
||
<A NAME="___________"></A>
|
||
<!-- BR>
|
||
|
||
<A NAME="QuickStartPrefatoryNote"></A>
|
||
|
||
<P class="indent40">
|
||
|
||
[IF LIGHT GREY BACKGROUND F5F5F5 IS USED INSTEAD OF WHITE,
|
||
CHANGE TO CELLPADDING=10 AROUND IMAGE]
|
||
|
||
<table style="margin:0px 0px 0px 0px;" width="800" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
||
<tr>
|
||
<td>
|
||
The illustration below shows the <B>easy, 1-2-3 step</B> process for using <A HREF="../vastplus.cgi">VAST+</A>. It uses an existing structure from MMDB (<A HREF="______">1XYZ: StructureName</A>) as the <A HREF="#Input">input</A>[<A HREF="test_input_files/__filename__.txt">sample input file of __________</A>] and retrieves _____________. Click on any panel of the image below to link to subsequent sections in this help document, which provide additional details about each step: <A HREF="#Input">(1) input</A>, <A HREF="#Output">(2) output</A>, and <A HREF="#ViewInCn3D">(3) 3D views</A>.
|
||
|
||
<BR><BR>
|
||
</td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
</P>
|
||
<BR -->
|
||
|
||
<!-- ================= QUICK_START_ILLUSTRATION ==================== -->
|
||
|
||
<A NAME="QuickStartIllustration"></A>
|
||
|
||
<!-- SINGLE IMAGE FILE; NOTE: IF LIGHT GREY BACKGROUND F5F5F5 IS USED INSTEAD OF
|
||
WHITE, CHANGE TO CELLPADDING=10 AROUND IMAGE -->
|
||
|
||
<!-- P class="indent40">
|
||
<table style="margin:0px 0px 0px 0px;" width="800" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
||
<tr>
|
||
<td ALIGN="center">
|
||
<IMG src="images/1_2_3_proteins_to_biosystems.png" width="800" height="605" border="0" align="center" alt="Illustration of the three steps in using FLink: (1) input UIDs for desired starting database, (2) review input list and select destination database, (3) retrieve ranked list of records from destination database.">
|
||
</td>
|
||
</tr>
|
||
</table>
|
||
</P -->
|
||
|
||
<!-- SEPARATE, CLICKABLE IMAGE FILE FOR EACH PART OF GRAPHIC -->
|
||
|
||
<!-- P class="indent40">
|
||
|
||
<table style="margin:0px 0px 0px 0px;" width="800" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
||
|
||
<tr>
|
||
<td ALIGN="center" colspan="5">
|
||
<A HREF="test_input_files/protein_sample_list_417_uids.txt"><IMG src="images/1_2_3_proteins_to_biosystems_0_banner_only.png" width="800" height="27" border="0" align="center" alt="Title banner for the Quick Start Guide illustration, which shows the three easy steps in using FLink. The featured example shows how to import a list of protein sequence GI numbers and retrieve a ranked list of BioSystems that contain those proteins. Click on this banner to open the sample input file of 417 protein GI numbers that was used to generate the step 1, 2, and 3 illustrations below. Save the file to your computer and import it into FLink to try the example yourself."></A>
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
<td ALIGN="center" colspan="5" class="NormalText">
|
||
<img SRC="../../IMG/spacer.gif" width="25" height="1" border="0">
|
||
</td>
|
||
</tr>
|
||
|
||
<tr>
|
||
|
||
<td ALIGN="center" class="NormalText">
|
||
<A HREF="#Input"><IMG src="images/1_2_3_proteins_to_biosystems_1_input_panel.png" width="251" height="565" border="0" align="center" alt="Step 1 in using FLink: Select the desired starting database and input a list of UIDs. Click on this graphic to read more details about input formats and options."></A>
|
||
</td>
|
||
|
||
<td ALIGN="center" class="NormalText">
|
||
<img SRC="../../IMG/spacer.gif" width="7" height="565" border="0">
|
||
</td>
|
||
|
||
<td ALIGN="center" class="NormalText">
|
||
<A HREF="#InputSummary"><IMG src="images/1_2_3_proteins_to_biosystems_2_review_and_select_panel.png" width="259" height="565" border="0" align="center" alt="Step 2 in using FLink: Review your input list and use the LinkTo menu option to select a destination database. Click on this graphic to read more details about this display, the JobID you'll receive after using the LinkTo option, and folder tab functions."></A>
|
||
</td>
|
||
|
||
<td ALIGN="center" class="NormalText">
|
||
<img SRC="../../IMG/spacer.gif" width="7" height="565" border="0">
|
||
</td>
|
||
|
||
<td ALIGN="center" class="NormalText">
|
||
<A HREF="#Output"><IMG src="images/1_2_3_proteins_to_biosystems_3_output_panel.png" width="276" height="565" border="0" align="center" alt="Step 3 in using FLink: View the output, which displays a ranked list of records from destination database. The frequency column shows the number of items from your input list that are linked to each retrieved record. Click on this graphic to read more details about the output display, its folder tab functions, and options to save the input and/or output list as a CSV file."></A>
|
||
</td>
|
||
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
</P -->
|
||
|
||
<!-- ================= END_QUICK_START_ILLUSTRATION ==================== -->
|
||
|
||
<!-- ================= QUICK_START_FOOTNOTE ==================== -->
|
||
|
||
<A NAME="QuickStartFootnote"></A>
|
||
|
||
<!-- P class="indent40">
|
||
|
||
<table style="margin:0px 0px 0px 0px;" width="800" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
||
<tr>
|
||
<td>
|
||
|
||
<tr>
|
||
<td>
|
||
|
||
<BR>
|
||
[Subsequent sections of this FLink help document provide additional details about the proper formatting of the <A HREF="#Input">input UID list</A> (part 1b of the graphic above) and the features of the <A HREF="#InputSummary">input summary display</A> (part 2a of graphic) and <A HREF="#Output">output display</A> (part 3 of graphic).<BR><BR>]
|
||
|
||
If you would like to try this example yourself, save the <A HREF="test_input_files/protein_sample_list_417_uids.txt">sample file of 417 protein sequence UIDs</A> that was used for this illustration to your computer. Then open the <A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A> home page, select "Protein" as the start database, upload the file, and follow the remaining steps illustrated above.
|
||
|
||
<I>(A corresponding textual step-by-step guide is provided in the guide on: "<A HREF="flink_how_to_proteins_to_biosystems.html">How to start with a list of proteins and find the biosystems in which they are involved</A>.")</I>
|
||
|
||
</td>
|
||
</tr>
|
||
|
||
</table>
|
||
|
||
</P>
|
||
<BR><BR -->
|
||
|
||
<!-- ================= END_QUICK_START_FOOTNOTE ==================== -->
|
||
|
||
<!-- ====== 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 MiniText"> </TD>
|
||
</TR>
|
||
</TABLE -->
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ########### BLUE_HEADER_SECTION_3_INPUT ############# -->
|
||
|
||
<A NAME="Input"></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">Input Options</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_INPUT ############ -->
|
||
|
||
|
||
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ########### -->
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" 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_THIS_SECTION ============== -->
|
||
<BR>
|
||
<BLOCKQUOTE><BLOCKQUOTE>
|
||
|
||
<A HREF="#InputID">PDB ID or MMDB ID</A> | <A HREF="#InputEntrezSearch">Structure or Protein database search</A> | <A HREF="#Input3Dcoordinates">3D coordinates</A>
|
||
|
||
</BLOCKQUOTE></BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
||
|
||
<!-- ============== LEVEL_1_INPUT_OPTION_1_PDB_ID_OR_MMDB_ID ================ -->
|
||
|
||
<A NAME="InputID"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>PDB ID or MMDB ID</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>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
If you know the <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvRecordIdentifiers">identifier</A> for a structure that is currently in the <A HREF="/structure/">Molecular Modeling Database (MMDB)</A> and would like to find its <A HREF="../vastplus.cgi">VAST+</A> similar structures, simply:<BR>
|
||
|
||
<UL>
|
||
|
||
<LI>Enter the <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvPDBID"><B>PDB ID</B></A> or <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMMDBID"><B>MMDB ID</B></A> for the structure of interest <B>directly into the</B> <A HREF="../vastplus.cgi"><B>VAST+</B></A> <B>home page</B>.</LI><BR>
|
||
|
||
<LI>VAST+ will then <A HREF="#Output">display</A> your <!-- A HREF="#OutputQueryStructure" -->query structure followed by a list of geometrically similar structures, <A HREF="#OutputRankedList">ranking</A> them by the extent of their similarity to the query structure's <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A>.</LI><BR>
|
||
|
||
<LI>A <A HREF="#GraphicalDisplays">detailed view</A> for each retrieved structure shows the correspondence between individual protein molecules in the query and subject structures. The "<A HREF="#3DView">3D View</A>" button enables you to view a superposition of the aligned regions.</LI><BR>
|
||
|
||
<LI>Please note that the latest release of <A HREF="/Structure/CN3D/cn3d.shtml "><B>Cn3D</B></A> (<B>version 4.3.1</B>) is necessary in order to properly view the superpositions.</LI><BR>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- =========== END_LEVEL_1_INPUT_OPTION_1_PDB_ID_OR_MMDB_ID ========== -->
|
||
|
||
|
||
<!-- ============== LEVEL_1_INPUT_OPTION_2_ENTREZ_SEARCH ============= -->
|
||
|
||
<A NAME="InputEntrezSearch"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Structure or Protein database search</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>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
If you don't know the <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvRecordIdentifiers">identifier</A> of a specific structure record, you can start by searching for a term(s) of interest (e.g., tumor suppressor, immunoglobulin) in the <A HREF="/structure/">Entrez Structure</A> or <A HREF="/protein/">Entrez Protein</A> database, then follow the links on the search results page from a structure or protein sequence of interest to "similar structures." There are several different ways this can be done:<BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="InputEntrezStructure2SimilarStructure"></A><B>3D structure → similar structures</B><!-- (geometrically similar) --></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>Search the <A HREF="/structure/"><B>Entrez Structure</B></A> database for a text word or phrase of interest.<BR>
|
||
For example, retrieve structures that contain the term <A HREF="/structure/?term=immunoglobulin">immunoglobulin</A>, or the phrase <A HREF="/structure/?term=%22tumor+suppressor%22">"tumor suppressor"</A>, anywhwere in the record. If desired, you can limit your query to a specific <A HREF="../../MMDB/docs/mmdb_help.html#SearchFields">search field</A> of the record, such as the title of the article describing the structure, for example: <A HREF="/structure/?term=%22tumor+suppressor%22%5Btitle%5D">"tumor suppressor"[title]</A> or <A HREF="/structure/?term=immunoglobulin%5Btitle%5D">immunoglobulin[title]</A>.
|
||
(The MMDB Help document provides <A HREF="../../MMDB/docs/mmdb_help.html#SearchTips">search tips</A> for the structure database.)</LI><BR>
|
||
|
||
<LI>On the <A HREF="../../MMDB/docs/mmdb_help.html#SearchResults"><B>Structure search results page</B></A>, click on the <B>thumbnail image</B> or <B>title</B> of a structure of interest to open its <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">summary page</A>, then press the "<B>Similar Structures: VAST+</B>" button near the upper right hand corner of the page.
|
||
</LI><BR>
|
||
|
||
<!-- UL>
|
||
<LI><B>Either</B> click the <B>check box</B> next to a structure of interest, then open the "<B>Find Related Data</B>" menu in the right hand margin, select "<B>Structure</B>," and press "<B>Find items</B>."<BR><BR>
|
||
<B><I>...or...</I></B></LI><BR>
|
||
|
||
<LI><B>Or</B> click on the <B>thumbnail image</B> or <B>title</B> of a structure of interest to open its <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">summary page</A>, then press the <B>VAST button</B> near the upper right hand corner of the page to open a list of structures that are similar in 3D shape to the one currently displayed.</LI><BR>
|
||
</UL -->
|
||
|
||
<LI>The resulting page will display the <A HREF="#Output">VAST+ search results</A>, listing structures that are <B>geometrically similar</B> to the structure you checked or viewed, <A HREF="#OutputRankedList">ranked</A> by the extent of their similarity to the query structure's <A HREF="#OutputBiologicalUnit">biological unit</A>.</LI><BR>
|
||
|
||
</UL>
|
||
|
||
|
||
<LI><A NAME="InputEntrezProtein2Structure2SimilarStructure"></A><B>protein sequence → structure<!-- (source structure) --> → similar structures</B><!-- (geometrically similar) --></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>Search the <A HREF="/protein/"><B>Entrez Protein</B></A> database for a text word or phrase of interest. (For tips on searching the Entrez Protein database, see <A HREF="/books/NBK3836/">Entrez Help</A>, <A HREF="/books/NBK44864/">Entrez Sequences Help</A>, and <A HREF="/books/NBK49541/">Entrez Nucleotide and Entrez Protein FAQs</A>.)</LI><BR>
|
||
|
||
<LI>On the <B>Protein search results page</B>, click on the <B>title</B> of a protein of interest to open its sequence record, then scroll down to the "<B>Related Information</B>" section in the right hand margin of the page. If the protein sequence was <I><B>derived from a 3D structure record</B></I>, the Related Information section will include "<B>Structure</B>." Select that option.</LI><BR>
|
||
|
||
<!-- UL>
|
||
<LI><B>Either</B> click the <B>check box</B> next to protein sequence of interest, then open the "<B>Find Related Data</B>" menu in the right hand margin. If the protein sequence was <I><B>derived from a 3D structure record</B></I>, the menu will include "<B>Structure</B>." Select that option and press "<B>Find items</B>" to retrieve the 3D structure record from which the protein sequence was derived. [Don't include this block of text because "Structure" will appear in the "Find Related Data" menu on the docsum page for any/all structure records, whether or not they were derived from structure records. The only way a user knows if a protein does indeed have a structure record is either by the accession number format, or by checking the box next to the protein sequence record of interest, selecting "Find related data: Structure," and then seeing if any records are retrieved. That's too much to explain and makes the system seem too complex, so just show the text in the next bullet point.]<BR><BR>
|
||
<B><I>...or...</I></B></LI><BR>
|
||
|
||
<LI><B>Or</B> click on the <B>title</B> of a protein of interest to open its sequence record, then scroll down to the <B>Related Information</B> section in the right hand margin of the page and select <B>Structure</B>.</LI><BR>
|
||
</UL -->
|
||
|
||
<LI>The resulting page will display the <I><B>3D structure record from which the protein sequence was derived</B></I>. From there, follow the link for "<B>Similar Structures: VAST+</B>" to see a list of geometrically similar structures identified by <A HREF="../vastplus.cgi">VAST+</A>.<!-- From here, you can follow links for "<B>Find Related Data: Structures</B>" or "<B>Similar Structures: VAST+</B>" (depending on which page view you are looking at) to see a list of geometrically similar structures identified by <A HREF="../vastplus.cgi">VAST+</A>. --></LI><BR>
|
||
|
||
<LI><I>Note: If the "Related Information" section of a protein sequence record does <B>not</B> list "Structure" as an option, then use the next method described below, to traverse from protein sequence → related structure → similar structures<!-- to traverse from a protein to a sequence-similar structure, and then to geometrically similar structures -->.</I></LI><BR>
|
||
|
||
</UL>
|
||
|
||
|
||
<LI><A NAME="InputEntrezProtein2RelatedStructure2SimilarStructure"></A><B>protein sequence → related structures<!-- (sequence-similar) --> → similar structures<!-- (geometrically similar) --></B></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>Only a small percentage of sequence records in the <A HREF="/protein/">Entrez Protein</A> database are derived from 3D structure records. However, it is still possible to find 3D structure records for the majority of protein sequence records by retrieving structures that are <B>sequence-similar</B> to your protein of interest. These are called "<B>Related Structures</B>" and they have been identified by a program called <A HREF="../../MMDB/mmdb.shtml#CBLAST">CBLAST</A>. From there, you can find geometrically similar structures that have been identified by VAST. To do this, follow these steps:</LI><BR>
|
||
|
||
<LI>Search the <A HREF="/protein/"><B>Entrez Protein</B></A> database for a text word or phrase of interest. (For tips on searching the Entrez Protein database, see <A HREF="/books/NBK3836/">Entrez Help</A>, <A HREF="/books/NBK44864/">Entrez Sequences Help</A>, and <A HREF="/books/NBK49541/">Entrez Nucleotide and Entrez Protein FAQs</A>.)</LI><BR>
|
||
|
||
<LI>On the <B>Protein search results page</B>, click on the <B>title</B> of a protein of interest to open its sequence record, then scroll down to the "<B>Related Information</B>" section in the right hand margin of the page. An option for "<B>Related Structures</B>" will be present if there are 3D structures that are <B>sequence-similar</B> to the protein currently displayed. Select that option.</LI><BR>
|
||
|
||
<LI>The resulting page will display a list of <I><B>3D structures that are sequence-similar</B></I> to your protein of interest. Click on the thumbnail of any structure to open its <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">summary page</A>.
|
||
From there, follow the link for "<B>Similar Structures: VAST+</B>" to see a list of geometrically similar structures identified by <A HREF="../vastplus.cgi">VAST+</A>.<!-- From here, you can follow links for "<B>Find Related Data: Structures</B>" or "<B>Similar Structures: VAST+</B>" (depending on which page view you are looking at) to see a list of geometrically similar structures identified by <A HREF="../vastplus.cgi">VAST+</A>. --></LI><BR>
|
||
|
||
<LI><I>Note: If the "Related Information" section of a protein sequence record <B>also</B> lists "Structure" as an option, that means the protein sequence was derived from a 3D structure record. In that case, you can also use the previous method for accessing 3D structures, if desired, to traverse from protein sequence → structure → similar structures.</I></LI><BR>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== BOXED_NOTE =============== -->
|
||
|
||
<A NAME="_______________"></A>
|
||
<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell" ALIGN="Center" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="10" class="WhiteCell NormalText3">
|
||
<TR>
|
||
<TD class="WhiteCell" WIDTH="70" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
<TD class="WhiteCellBlueEdgeAll" ALIGN="Left" VALIGN="TOP">
|
||
<P class="indent20bottomspace NormalText3"><P class="pad10"><B>Tip</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 text text text text text.</P>
|
||
</TD>
|
||
<TD class="WhiteCell" WIDTH="70" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR -->
|
||
|
||
<!-- ================== END_BOXED_NOTE =============== -->
|
||
|
||
<!-- ============== END_LEVEL_1_INPUT_OPTION_2_ENTREZ_SEARCH =========== -->
|
||
|
||
|
||
<!-- =========== LEVEL_1_INPUT_OPTION_3_3D_COORDINATES =========== -->
|
||
|
||
<A NAME="Input3Dcoordinates"></A>
|
||
<A NAME="3Dcoordinates"></A>
|
||
<A NAME="InputVASTSearch"></A>
|
||
<A NAME="VASTSearch"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>3D coordinates of a query 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>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
The <A HREF="#Input">methods</A> described above for accessing similar structures (enter a <A HREF="#InputID">PDB ID or MMDB ID</A>, or start with a <A HREF="#InputEntrezSearch">Structure or Protein database search</A>) will work if your query structure of interest <B>is already available</B> in the <A HREF="../../MMDB/mmdb.shtml">Molecular Modeling Database (MMDB)</A>, and they retrieve <B>pre-computed</B> VAST+ results.<BR><BR>
|
||
|
||
If your query structure <B>is not yet available</B> in <A HREF="../../MMDB/mmdb.shtml">MMDB</A>, then you can use <A HREF="../../VAST/vastsearch.html"><B>VAST Search</B></A> to find 3D similar structures. VAST Search allows you to <B>input the 3D coordinates</B> of a newly resolved structure (in <A HREF="http://www.wwpdb.org/docs.html">PDB format</A>) and compare it, in a <B>live search</B>, against all structures in MMDB to find its neighbors. A separate <A HREF="../../VAST/vastsrchelp.html"><B>VAST Search Help</B></A> document provides additional details.<BR><BR>
|
||
|
||
Please note that, at this time, <A HREF="../../VAST/vastsearch.html">VAST Search</A> still returns results in the <A HREF="#OriginalVASTDisplay"><B>original VAST format</B></A>, listing structures that have similarities to <B>individual protein molecules</B> in your query structure. Although some of the returned structures might also have a <B>biological unit</B> that is similar to the query, the original style VAST results does not group results by biological unit similarity.<BR><BR>
|
||
|
||
If you eventually submit your query structure to the Protein Data Bank (PDB), once your structure is publicly released by PDB, it will also become available in MMDB. At MMDB, your structure's VAST neighbors will be pre-computed (as part of the <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing">MMDB data processing</A> procedure), grouped by biological unit similarity (complete or partial biological unit similarity), and <A HREF="#OutputRankedList">ranked</A> by the number of protein molecules in the query that simultaneously match the 3D shape of protein molecules in the VAST+ neighbor. Its VAST+ neighbors will then become accessible through the <A HREF="#Input">methods</A> described above, and will be presented in the <A HREF="#IllustratedExample1B26"><B>new style VAST+ display</B></A> described in this document.<BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- ============== END_LEVEL_1_INPUT_OPTION_3_3D_COORDINATES ============= -->
|
||
|
||
|
||
<!-- ====== 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 MiniText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ########### BLUE_HEADER_SECTION_4_OUTPUT ############# -->
|
||
|
||
<A NAME="Output"></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">Output</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_OUTPUT ############ -->
|
||
|
||
|
||
<!-- ########## 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_THIS_SECTION ============== -->
|
||
<BR>
|
||
<BLOCKQUOTE>
|
||
|
||
<A HREF="#OutputQueryStructure">query structure</A> | <A HREF="#OutputSimilarStructures">similar structures</A> | <A HREF="#OutputFilters">filters</A> (<A HREF="#OutputFilterCompleteMatch"><IMG SRC="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 biounit matches</A>, <A HREF="#OutputFilterPartialMatch"><IMG SRC="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 biounit matches</A>, <A HREF="#OutputFilterTaxonomy">taxonomy</A>) | <A HREF="#OutputFolderTabs">folder tabs to select 3D alignment type</A> (<A HREF="#OutputFolderTabInitialAlignment">all matching molecules superposed</A>, <A HREF="#OutputFolderTabRefinedAlignment">invariant substructure superposed</A>) | <A HREF="#OutputRankedList">ranked list of hits</A> (<A HREF="#OutputSortOptions">sort options</A>, <A HREF="#OutputViewDetails">view details for a similar structure</A>, <A HREF="#OutputSearchWithinResults">search within results</A><!-- A HREF="#OutputSave">save results as CSV file</A -->) | <A HREF="#OutputOriginalVASTButton">"original VAST" button</A> | <A HREF="#NullResult">null result: "no matched structure found"</A> | <A HREF="#OutputNewSearchButton">"new search" button</A>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
||
|
||
<!-- ======== LEVEL_1_OUTPUT_INTRO_NOTE =========== -->
|
||
|
||
<P class="indent20">
|
||
<A NAME="OutputIntroNote"></A>
|
||
<!-- The VAST+ search results page displays summary information about your <A HREF="#OutputQueryStructure"><B>query structure</B></A>, followed by a <A HREF="#OutputRankedList"><B>ranked list</B></A> of structures that are similar in 3D shape to the query structure you specified, with an emphasis on those that have a macromolecular complex (<A HREF="#OutputBiologicalUnit"><B>biological unit</B></A>) similar to the query <I>(<A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span></A>)</I>. -->
|
||
|
||
<A NAME="OutputIntroNote"></A>
|
||
The VAST+ search results page displays summary information about your <A HREF="#OutputQueryStructure"><B>query structure</B></A>, followed by a list of <B>similar structures</B> that are <A HREF="#OutputRankedList"><B>ranked</B></A> based on their degree of similarity to the query structure's macromolecular complex (<!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit"><B>biological unit</B></A>) <I>(<A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span></A>)</I>.
|
||
|
||
By default, all similar structures are listed, starting with <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."><B>complete matches</B></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."><B>partial matches</B></A>, and ending with matches to individual protein molecules.
|
||
If desired, you can activate a subset of <A HREF="#Filters"><B>filters</B></A> in order to display only the subset of similar structures that meet the specified criteria. It is also possible to change the <A HREF="#OutputSortOptions"><B>sort order</B></A> of the similar structures, and to <A HREF="#OutputSearchWithinResults"><B>search within results</B></A> to see if/where a specific structure falls within the search results.
|
||
Click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit."> beside any structure to see a <A HREF="#GraphicalDisplays"><!-- A HREF="#QuerySubjectComparison" --><B>detailed view comparing the query structure to a matched structure</B></A>. <I>(If you prefer to view your search results in the original style VAST display, which lists structures that have similarities to individual protein molecules, or similarities to individual <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domains</A>, in your query structure, click the "<A HREF="#OutputOriginalVASTButton">Original VAST</A>" button.)</I><BR><BR>
|
||
<!-- To begin a new search with a different query structure, enter the desired PDB ID or MMDB ID in the <A HREF="#OutputNewSearchButton">New Search</A> text box that appears in the upper right corner of the VAST+ search results page.<BR><BR -->
|
||
|
||
A VAST+ search results page includes the following components:<BR><BR>
|
||
</P>
|
||
|
||
|
||
<!-- ======== END_LEVEL_1_OUTPUT_INTRO_NOTE =========== -->
|
||
|
||
<!-- ======== LEVEL_1_OUTPUT_QUERY_STRUCTURE_SUMMARY_INFO =========== -->
|
||
|
||
<A NAME="OutputQueryStructure"></A>
|
||
<A NAME="QueryStructure"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Query structure (summary 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>
|
||
<BR>
|
||
|
||
<!-- ============ PREFATORY_NOTE ============== -->
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
The <B>top section</B> of a VAST+ results display provides the following summary information about the <B>query structure</B>, including:<BR><BR>
|
||
|
||
<A HREF="#OutputInteractionsSchematic">interactions schematic</A> |
|
||
<A HREF="#OutputMolecularGraphic">molecular graphic</A> |
|
||
<A HREF="#OutputMMDBID">MMDB ID</A>, <A HREF="#OutputPDBID">PDB ID</A> |
|
||
<A HREF="#OutputBiologicalUnit">biological unit</A> |
|
||
<A HREF="#OutputSourceOrganism">source organism</A> |
|
||
<A HREF="#OutputNumberOfProteins">number of proteins</A> |
|
||
<A HREF="#OutputNumberOfNucleotides">number of nucleotides</A> |
|
||
<A HREF="#OutputNumberOfChemicals">number of chemicals</A>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ========== END_PREFATORY_NOTE ============ -->
|
||
|
||
<!-- ========== 2_COLUMN_TABLE =============== -->
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="format1 TableText1" width="90%" border="black 1px" cellpadding="4">
|
||
|
||
<!-- TR>
|
||
<TD class="format1H" align="left" style="white-space: nowrap;"><b>__HeaderForColumn1___</b></TD>
|
||
<TD class="format1H" align="center" style="white-space: nowrap;"><b>__HeaderForColumn2___</b></TD>
|
||
</TR -->
|
||
|
||
<!-- ============= INTERACTIONS_SCHEMATIC ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" width="180" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="OutputInteractionsSchematic"></A><A NAME="OutputInteractionSchematic"></A><A NAME="QueryStructureInteractionsSchematic"></A><A NAME="QueryStructureInteractionSchematic"></A><A NAME="InteractionSchematic"></A><A NAME="InteractionsSchematic"></A><A NAME="Interactions"></A><B>Interactions schematic</B><BR><BR>
|
||
<IMG SRC="images/1HBB_interaction_schematic.png" WIDTH="150" HEIGHT="150" BORDER="0" ALT="interaction schematic for 1HBB: High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site (human hemoglobin)."></TD>
|
||
<TD class="format1A" valign="top">The interactions schematic shows the <!-- A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents" -->molecular components of the <B>query structure's</B> <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A> and the <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingInteractions">interactions</A> among them.
|
||
<A NAME="MolecularComponents"></A>
|
||
The <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents">molecular components</A> 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="../../MMDB/docs/mmdb_help.html#MmdbsrvProteins">Proteins</A>, if present, are shown as circles:</TD>
|
||
<TD WIDTH="80" ALIGN="LEFT" VALIGN="TOP"><A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvProteins"><IMG SRC="../../MMDB/docs/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"></IMG></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="430" ALIGN="LEFT" VALIGN="TOP"><A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvNucleotides">Nucleotide sequences</A> (DNA, RNA), if present, are shown as squares:</TD>
|
||
<TD WIDTH="80" ALIGN="LEFT" VALIGN="TOP"><A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvNucleotides"><IMG SRC="../../MMDB/docs/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"></IMG></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD WIDTH="430" ALIGN="LEFT" VALIGN="TOP"><A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvChemicals">Chemicals</A>, if present, are shown as diamonds:</TD>
|
||
<TD WIDTH="80" ALIGN="LEFT" VALIGN="TOP"><A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvChemicals"><IMG SRC="../../MMDB/docs/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"></IMG></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="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalFormsCrystalSymmetry">crystallographic symmetry</A>, their labels are shown as alphanumeric combinations (for example, <IMG SRC="../../MMDB/docs/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="../../MMDB/docs/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.</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
The protein and nucleotide icons are scaled to show the relative sizes 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>
|
||
|
||
<A NAME="MmdbsrvThumbnailSchematicInteractions"></A>
|
||
<A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingInteractions">Interactions</A> among components are shown as <B>lines</B>, and an interaction is displayed only if there are <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingInteractionsContactNumberThreshold">at least 5 contacts</A> at a distance of <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingInteractionsDistanceThreshold">4 Å or less</A> between the heavy atoms of the molecules. <I>(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.)</I><BR><BR>
|
||
|
||
Because of the latter thresholds, <B>ions</B> that are part of the <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A> may be missing from the interaction diagram, but they will be listed in the table of <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents">molecular components and interactions</A> on the query structure's <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">MMDB summary page</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.<BR><BR>
|
||
|
||
<B>Mouse over any node in the schematic</B> 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="../../MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents">molecular components</A>.}} --><BR><BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ============= MOLECULAR_GRAPHIC ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="OutputMolecularGraphic"></A><A NAME="QueryStructureMolecularGraphic"></A><B>Molecular graphic</B><BR><BR>
|
||
<IMG SRC="images/1HBB_molecular_graphic.png" WIDTH="150" HEIGHT="150" BORDER="0" ALT="Molecular graphic for 1HBB: High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site (human hemoglobin)."></TD>
|
||
<TD class="format1A" valign="top">The 3D molecular graphic shows a single static snapshot of the query structure's 3D shape, generated by the <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> program.
|
||
|
||
<A NAME="MmdbsrvThumbnailMolecularGraphicBiologicalForm"></A>
|
||
In general, it shows the default <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A> of the structure.<!-- I>(See the MMDB help document for <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvThumbnailMolecularGraphic">additional information</A> about molecular graphic thumbnail images.)</I --><BR><BR>
|
||
|
||
To view the query's 3D structure interactively, click on its MMDB ID. That will open the corresponding <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">structure summary</A> page in MMDB, where you can choose to "View structure."<BR><BR>
|
||
|
||
To view a 3D superposition of the query structure and any one of the VAST+ hits, <SPAN style="background-color: #FFFF00">Click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit."></SPAN> beside a hit to open the <A HREF="#QuerySubjectComparison">detailed view comparing the query structure to a matched structure</A>, then click the "<A HREF="#3DView">Visualize 3D structure superposition with Cn3D</A>" button at the bottom of that view.<BR><BR>
|
||
|
||
In either case, the interactive 3D view will open in <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A>, NCBI's WebGL-based viewer.<BR><BR>
|
||
|
||
There is no need to install a separate application in order to use iCn3D; you just need to use a <B><I>web browser that supports <A HREF="https://get.webgl.org/">WebGL</A></I></B>. If your browser doesn't support WebGL, you might need to modify the settings in the browser to enable WebGL, or 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.)<BR><BR>
|
||
|
||
|
||
<!-- In either case, NCBI's free <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> program must be installed on your computer and configured as a helper application for your browser in order for the "View structure" or "3D View" buttons to open the 3D structure. -->
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ============= MMDB ID and PDB ID ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="OutputMMDBID"></A><A NAME="QueryStructureMMDBID"></A><B>MMDB ID</B> and <A NAME="OutputPDBID"></A><A NAME="QueryStructurePDBID"></A><B>PDB ID</B></TD>
|
||
<TD class="format1A" valign="top">
|
||
|
||
<B>MMDB ID</B> is the unique identifier of the structure record in the <A HREF="/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="../../MMDB/docs/mmdb_help.html#SearchFieldUID">UID</A>.) --><BR><BR>
|
||
|
||
<B>PDB ID</B> is the accession of number of the <A HREF="http://www.rcsb.org/pdb/">Protein Data Bank (PDB)</A> record from which the corresponding 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>).<BR><BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ============= BIOLOGICAL UNIT ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="BiologicalUnit"></A><A NAME="BioUnit"></A><A NAME="OutputBiologicalUnit"></A><A NAME="QueryStructureBiologicalUnit"></A><B>Biological Unit</B></TD>
|
||
|
||
<TD class="format1A" valign="top">The <B>biological unit</B> ("<B>biounit</B>") of a structure is the <B>biochemically active form of a biomolecule</B>. It can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules, and is sometimes also referred to as the "biological assembly" or "<B>macromolecular complex</B>," reflecting the molecule's <A HREF="../../MMDB/docs/mmdb_help.html#FourLevelsOfStructure">quaternary structure</A>.<BR><BR>
|
||
|
||
The <B>query structure's biological unit</B>, if available, is included in the summary information at the top of a VAST+ results page. (To see the biological unit of any individual VAST neighbor, and other details about the match, click on the plus button <A HREF="#QuerySubjectComparison"><IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit. Click on this image to read more about the expanded view."></A> beside the structure of interest.)<!-- (To see the biological units of the similar structures that were found by VAST+, click on the + beside an individual structure of interest to see details about the match.) --><BR><BR>
|
||
|
||
The <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing">data processing</A> section of the MMDB help document provides additional information about <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms">biological units</A>, incuding the <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalFormsProcedures">procedures used to identify biological units</A>.<BR><BR>
|
||
|
||
If the query structure does <B>not</B> have a biological unit defined in its source PDB file, it is only available as an <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A> (i.e., raw structure data). In that case, the structure is not processed by VAST+, since VAST+ focuses on finding similarities among biological units. However, such structures are processed by the <A HREF="#OriginalVAST">Original VAST</A> algorithm, which may have found structures that are geometrically similar to individual proteins, or individual <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domains</A>, in your query. <I>(Read more about the occasional cirsumstances in which a query structure might generate a <A HREF="#NullResult">null result</A> in VAST+).</I><BR><BR>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ============= SOURCE ORGANISM ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="OutputSourceOrganism"></A><A NAME="QueryStructureSourceOrganism"></A><B>Source Organism</B></TD>
|
||
<TD class="format1A" valign="top">The source organism(s) of the <A HREF="../../MMDB/docs/mmdb_help.html#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="/structure?cmd=search&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="/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>
|
||
|
||
<!-- ============= NUMBER OF PROTEINS ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="OutputNumberOfProteins"></A><A NAME="QueryStructureNumberOfProteins"></A><B>Number of proteins</B></TD>
|
||
<TD class="format1A" valign="top">The total number of protein molecules in the <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><!-- A HREF="#OutputBiologicalUnit" --><A HREF="#BiologicalUnit">biological unit</A> of the query structure.<BR>
|
||
For brevity, only the first protein name is displayed by default.<BR>
|
||
Click on the down arrow <IMG SRC="images/arrow_blue_expand.png" WIDTH="13" HEIGHT="11" BORDER="0" ALT="Down arrow action button that enables you to view the complete list of protein molecules, nucleotide molecules, or chemicals in the biological unit of a structure."> to view the complete list of proteins in the biological unit.
|
||
<BR><BR>
|
||
The MMDB help document provides additional information about the <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents">molecular components</A> of a structure, incuding its <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvProteins">proteins</A>.</TD>
|
||
</TR>
|
||
|
||
<!-- ============= NUMBER OF NUCLEOTIDES ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="OutputNumberOfNucleotides"></A><A NAME="QueryStructureNumberOfNucleotides"></A><B>Number of nucleotides</B></TD>
|
||
<TD class="format1A" valign="top">The total number of nucleotide molecules (DNA and/or RNA) in the <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><!-- A HREF="#OutputBiologicalUnit" --><A HREF="#BiologicalUnit">biological unit</A> of the query structure.<BR>
|
||
For brevity, only the first nucleotide molecule's name is displayed by default.<BR>
|
||
Click on the down arrow <IMG SRC="images/arrow_blue_expand.png" WIDTH="13" HEIGHT="11" BORDER="0" ALT="Down arrow action button that enables you to view the complete list of protein molecules, nucleotide molecules, or chemicals in the biological unit of a structure."> to view the complete list of nucleotide molecules in the biological unit.
|
||
<BR><BR>
|
||
The MMDB help document provides additional information about the <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents">molecular components</A> of a structure, incuding its <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvNucleotides">nucleotide sequences</A>.
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ============= NUMBER OF CHEMICALS ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="OutputNumberOfChemicals"></A><A NAME="QueryStructureNumberOfChemicals"></A><B>Number of chemicals</B></TD>
|
||
<TD class="format1A" valign="top">The total number of chemicals in the <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><!-- A HREF="#OutputBiologicalUnit" --><A HREF="#BiologicalUnit">biological unit</A> of the query structure.<BR>
|
||
For brevity, only the first chemical name is displayed by default.<BR>
|
||
Click on the down arrow <IMG SRC="images/arrow_blue_expand.png" WIDTH="13" HEIGHT="11" BORDER="0" ALT="Down arrow action button that enables you to view the complete list of protein molecules, nucleotide molecules, or chemicals in the biological unit of a structure."> to view the complete list of chemicals in the biological unit.
|
||
<BR><BR>
|
||
The MMDB help document provides additional information about the <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents">molecular components</A> of a structure, incuding its <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvChemicals">chemicals</A>.
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- ============= XXXXXX ============== -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="Output_____"></A><A NAME="QueryStructure______"></A>______Column1__________</TD>
|
||
<TD class="format1A" valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= XXXXXX_WITH_UP_ARROW ============== -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1">
|
||
<A NAME="Output_____"></A><A NAME="QueryStructure______"></A>______Column1__________</TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></IMG></A>
|
||
______Column2__________<BR><BR>
|
||
</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>
|
||
<BR>
|
||
|
||
<!-- ============= END_2_COLUMN_TABLE ================ -->
|
||
|
||
<!-- ========== END_LEVEL_1_OUTPUT_QUERY_STRUCTURE_SUMMARY_INFO ========== -->
|
||
|
||
|
||
<!-- ======== LEVEL_1_OUTPUT_SIMILAR_STRUCTURES =========== -->
|
||
|
||
<A NAME="OutputSimilarStructures"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Similar Structures</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>
|
||
<BR>
|
||
|
||
<!-- ============ PREFATORY_NOTE ============== -->
|
||
<BLOCKQUOTE>
|
||
The <A HREF="../vastplus.cgi">VAST+</A> search results appear immediately beneath the query structure summary information, and include the following features and functions:
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="#OutputFolderTabs"><B>Folder tabs to select 3D alignment type:</B></A></LI>
|
||
<UL>
|
||
<LI><A HREF="#OutputFolderTabInitialAlignment">All matching molecules superposed</A></LI>
|
||
<LI><A HREF="#OutputFolderTabRefinedAlignment">Invariant substructure superposed</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#OutputFilters"><B>Filters</B></A> to subset the results by:</LI>
|
||
<UL>
|
||
<LI><A HREF="#OutputFilterMatchedMolecules">number of matching molecules</A></LI>
|
||
<UL>
|
||
<LI><A HREF="#OutputFilterCompleteMatch"><IMG SRC="images/icon_red_circle_solid.png" WIDTH="12" HEIGHT="12" 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 match to biological unit of query structure</A></LI>
|
||
<LI><A HREF="#OutputFilterPartialMatch"><IMG SRC="images/icon_red_circle_half_filled.png" WIDTH="12" HEIGHT="12" 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 match to biological unit of query structure</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#OutputFilterTaxonomy">taxonomy</A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#OutputRankedList"><B>Ranked list of hits</B></A>: a table listing similar structures ranked by the extent of their similarity to the query structure's biological unit.</LI>
|
||
<UL>
|
||
<LI><A HREF="#OutputSortOptions"><B>Sort Options</B></A></LI>
|
||
<UL
|
||
<LI><A HREF="#SortOptionAlignedProteins">Aligned proteins</A></LI>
|
||
<LI><A HREF="#SortOptionRMSD">RMSD</A></LI>
|
||
<LI><A HREF="#SortOptionAlignedResidues">Aligned residues</A></LI>
|
||
<LI><A HREF="#SortOptionSequenceIdentity">Sequence identity</A></LI>
|
||
</UL>
|
||
<LI><A HREF="#OutputViewDetails"><B>View details</B> for a similar structure</A></LI>
|
||
<LI><A HREF="#OutputSearchWithinResults"><B>Search within results</B></A></LI>
|
||
</UL>
|
||
|
||
<LI><A HREF="#OutputOriginalVAST"><B>"Original VAST"</B> button</A></LI>
|
||
|
||
<LI><A HREF="#OutputNoMatchedStructureFound"><B>"No matched structure found"</B></A></LI>
|
||
|
||
<LI><A HREF="#OutputNewSearchButton"><B>"New Search"</B> button</A></LI>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ========== END_PREFATORY_NOTE ============ -->
|
||
|
||
<!-- ============== OUTPUT_FOLDER_TABS ================ -->
|
||
|
||
<A NAME="OutputFolderTabs"></A>
|
||
<A NAME="DisplayFolderTabs"></A>
|
||
<A NAME="FolderTabs"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<SPAN class="HeaderText3"><B>Folder tabs to select 3D alignment type</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>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
The <A HREF="#Algorithm">VAST algorithm</A> calculates two different types of 3D alignments between a pair of similar structures: an <A HREF="#AlgorithmAlignmentInitial"><B>initial alignment</B></A> that shows <B>all matching molecules superposed</B>, and a <A HREF="#AlgorithmAlignmentRefined"><B>refined alignment</B></A> that shows the <B>invariant substructure superposed</B>.<BR><BR>
|
||
|
||
Each of the following folder tabs on the VAST+ output page includes the complete set of search results, listing all of structures that VAST+ found to be similar to your query structure.<BR><BR>
|
||
|
||
However, a given structure might have a different rank in the first tab versus the second tab, because the statistics generated for that match (e.g., <A HREF="#SortOptionRMSD">RMSD</A> and number of <A HREF="#SortOptionAlignedResidues">aligned residues</a>) generally differ between the two alignment types, and those statistics are used to determine the <A HREF="#OutputRankedList">sort order</A> of the search results.<BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="OutputFolderTabInitialAlignment"></A><A NAME="FolderTabInitialAlignment"></A><B>All matching molecules superposed</B> (initial alignment)</LI><BR>
|
||
|
||
<UL>
|
||
<LI>When you click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit."> beside any structure</B> to see a detailed view/graphical display comparing the query structure to the matched structure, the "<B>visualize 3D structure superposition</B>" button will open the <I>initial 3D alignment</I>, with <B>all matching molecules superposed</B>. The <A HREF="#Algorithm">VAST algorithm</A> section of this document provides <A HREF="#AlgorithmAlignmentInitial">more details about the initial alignment</A> as well as an example.</LI><BR>
|
||
</UL>
|
||
|
||
<LI><A NAME="OutputFolderTabRefinedAlignment"></A><A NAME="FolderTabInitialAlignment"></A><B>Invariant substructure superposed</B> (refined alignment)</LI><BR>
|
||
|
||
<UL>
|
||
<LI>When you click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit."> beside any structure</B> to see a detailed view/graphical display comparing the query structure to the matched structure, the "<B>visualize 3D structure superposition</B>" button will open the <I>refined 3D alignment</I>, with the <B>invariant substructure superposed</B>. The <A HREF="#Algorithm">VAST algorithm</A> section of this document provides <A HREF="#AlgorithmAlignmentRefined">more details about the refined alignment</A> as well as an example.</LI><BR>
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ============== END_OUTPUT_FOLDER_TABS ================ -->
|
||
|
||
<!-- ============== OUTPUT_FILTERS ================ -->
|
||
|
||
<A NAME="OutputFilters"></A>
|
||
<A NAME="DisplayFilters"></A>
|
||
<A NAME="Filters"></A>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<SPAN class="HeaderText3"><B>Filters to subset the search results<!-- Bar Graphs that characterize/filter the search 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><BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
An option to <B>Display Filters</B> appears above the ranked list of similar structures. This option generates <B>bar graphs</B> that: (1) provide <B>aggregate information</B> about the structures; (2) <B>categorize</B> the retrieved structures by their degree of similarity to the query structure and their taxonomic distribution; and (3) enable you to <B>subset</B> the results.<BR><BR>
|
||
|
||
By default, all similar structures are listed in the results display. Activate the <B>check boxes</B> beside one or more bar graphs to view only the subset of similar structures that meet the criteria you selected. <I>(Note: Selecting all of the check boxes is the same as selecting none (default), and will display the complete set of results. Selecting a subset of the checkboxes will display the subset of results that meet the desired criteria.)</I><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="OutputFilterMatchedMolecules"></A><A NAME="FilterMatchedMolecules"></A><B>Filter by number of matching molecules</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></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="OutputFilterCompleteMatch"></A><A NAME="FilterCompleteMatch"></A> <IMG SRC="images/icon_red_circle_solid.png" WIDTH="14" HEIGHT="14" 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."> <B>Complete match to biological unit of query structure</B> -- Each of the <A HREF="#Biopolymer">biopolymer</A> molecules<!-- (that meet the minimum size requirement for VAST) --> in the <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><!-- A HREF="#OutputBiologicalUnit" --><A HREF="#BiologicalUnit">biological unit</A> of the query structure have a match (i.e., are similar in 3D shape) to a biopolymer molecule in the subject. The <I><A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span> of VAST+ results</A></I> include complete matches, which are indicated by <B>solid red circles</B>.</LI><BR>
|
||
|
||
<LI><A NAME="OutputFilterPartialMatch"></A><A NAME="FilterPartialMatch"></A><IMG SRC="images/icon_red_circle_half_filled.png" WIDTH="14" HEIGHT="14" 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."> <B>Partial match to biological unit of query structure</B> -- A subset of the <A HREF="#Biopolymer">biopolymer</A> molecules, or an individual biopolymer molecule, from the <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><!-- A HREF="#OutputBiologicalUnit" --><A HREF="#BiologicalUnit">biological unit</A> of the query structure have a match (i.e., are similar in 3D shape) to a biopolymer molecule in the subject. The <I><A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span> of VAST+ results</A> include partial matches, which are indicated by <B>half-filled red circles</B>.</LI><BR>
|
||
|
||
<LI><I><B>Additional notes about matching molecules:</B></I>
|
||
<!-- If a structure contains a protein molecule that does not meet the minimum size requirement of 10 or more amino acids long with 3 or more <A HREF="../../MMDB/docs/mmdb_help.html#FourLevelsOfStructure">secondary structures</A>, that short protein will not be operated on by VAST, and will therefore not be considered in the VAST+ results. --></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="Biopolymer"></A><B>Biopolymers</B> refer to <B>protein</B>, <B>DNA</B>, and <B>RNA</B> molecules.
|
||
</LI><BR>
|
||
|
||
<LI><B>At this time, VAST (and VAST+) operates only on protein molecules</B>. Some biological units might contain other types of biopolymers as well, such as <B>DNA</B> or <B>RNA</B> molecules. VAST and VAST+ do not currently compute similarities between the 3D shapes of DNA molecules, or similarities between the 3D shapes of RNA molecules.<BR>
|
||
<BLOCKQUOTE>
|
||
<I><B>Example</B>: <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=103701"><B>1TUP</B></A>, "Tumor Suppressor P53 Complexed With DNA," has a pentameric biological unit composed of three proteins and two nucleotide sequences. VAST will find other structures that have similarly shaped proteins, but will not take the DNA molecules into consideration. Therefore, there will be <B>no "complete match"</B> structures in the <A HREF="/Structure/vastplus/vastplus.cgi?uid=1TUP">VAST+ search results for 1TUP</A></A>, as it is not currently possible to find a match for all five molecules in the biological unit. The top scoring hits, which match all three protein molecules in 1TUP, are nevertheless easy to find as they are displayed at the top of the <B>"partial match"</B> results, based on the default <A HREF="#SortOrder">sort order</A>.</I></BLOCKQUOTE>
|
||
</LI>
|
||
|
||
<LI><B>Mimimum size of protein:</B> VAST does not act upon protein molecules that have fewer than three <A HREF="../../MMDB/docs/mmdb_help.html#FourLevelsOfStructure"><B>secondary structure elements</B></A> (SSE's: alpha helices and/or beta sheets) <!-- and/or fewer than 10 amino acids -->because they can generate spurious hits. Such short proteins are therefore not considered in VAST+ calculations or results. For example, if a pentameric structure contains four large proteins, plus one small protein that doesn't meet the VAST size requirements, VAST will only operate on the four large proteins from the biological unit. Therefore, there will be no "complete match" structures in the VAST+ search results, and the top hits will be, at the most, structures that match all four long proteins.
|
||
<BLOCKQUOTE>
|
||
<I><B>Example</B>: <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=105549"><B>2YPL</B></A>, "Structural Features Underlying T-cell Receptor Sensitivity to Concealed MHC Class I Micropolymorphisms," contains four human proteins, plus one very small HIV protein. None of the structures in the <A HREF="/Structure/vastplus/vastplus.cgi?uid=2YPL">VAST+ search results for 2YPL</A> are listed as a complete hit, because the fifth protein in the 2YPL's biological unit does not meet the minimum size requirements for VAST. So the best possible match that VAST (and VAST+) can find is to 4 out of 5 proteins in the query structure's biological unit, and the top hits will be structures that, at the most, match all four of the long proteins. Each of those hits will be listed as a <B>"partial match."</B></I></BLOCKQUOTE>
|
||
</LI>
|
||
|
||
<LI><B>Pairwise alignments between individual protein components</B> of the query structure and subject are compared to each other for compatibility, and compatible/matching alignments are clustered into sets of alignments that together constitute a biological unit match. Pairwise alignments are compatible: (1) if they do not share the same macromolecules, i.e., an individual protein molecule from the query structure structure cannot be aligned to two or more protein molecules from the subject at the same time; and (2) if they generate similar instructions (spatial transformation matrices) for the superpositions of co-ordinate sets. A simple distance metric can be used to compare transformation matrices, and it lends itself to cluster alignment sets efficiently.</LI><BR><BR>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
<LI><A NAME="OutputFilterTaxonomy"></A><A NAME="FilterTaxonomy"></A><B>Filter by Taxonomy</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></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><B>Filter results by domain (superkingdom)</B> -- The "Filter by Taxonomy" options enable you to view the subset of similar structures from the "Eukaryota," "Bacteria," or "Archaea" domains (superkingdoms), from "Viruses," or from "Other" groups (such as synthetic constructs). Activate the check box(es) beside the group(s) of interest to see only the desired subset(s) of similar structures.<BR><BR>
|
||
|
||
Note that a taxonomy filter will retrieve structures in which <B>all biomolecules</B> in the structure are from the selected superkingdom. For example, the "Viruses" filter will retrieve structures that only contain molecules from viruses, and not molecules from any other superkingdom. Structures that are composed of synthetic constructs, or composed of molecules from two or more superkingdoms, are included in the "<B>Others</B>" taxonomy category. For example, PDB ID <a HREF="/Structure/mmdb/mmdbsrv.cgi?uid=4N9F">4N9F</a> would be classified with a taxonomy of "Others" because it includes molecules from Human immunodeficiency Virus 1 and Homo sapiens, which fall into the superkingdoms of Viruses and Eukaryota, respectively.</LI><BR>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ======== BOXED_NOTE_OUTPUT_FILTERS_ILLUSTRATED_EXAMPLE ======== -->
|
||
|
||
<A NAME="OutputFiltersIllustration"></A>
|
||
<!-- {TABLE width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell" ALIGN="Center" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="10" class="WhiteCell NormalText3">
|
||
<TR>
|
||
<TD class="WhiteCell" WIDTH="40" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
<TD class="WhiteCellBlueEdgeAll" ALIGN="Left" VALIGN="TOP">
|
||
<P class="indent20bottomspace NormalText3"><P class="pad10"><B>Example</B> - Bar graphs showing aggregate information about search results (as of 06 November 2013) for<BR><A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113"><B>High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site:<BR><BR>
|
||
<IMG SRC="images/______" WIDTH="600" HEIGHT="200" BORDER="0" ALT="________"><BR>
|
||
<A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB ">open a live web page with VAST+ results for 1HBB</A></P>
|
||
</TD>
|
||
<TD class="WhiteCell" WIDTH="40" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR} -->
|
||
|
||
<!-- ======== END_BOXED_NOTE_OUTPUT_FILTERS_ILLUSTRATED_EXAMPLE ======== -->
|
||
|
||
<!-- =============== END_LEVEL_1_OUTPUT_FILTERS =============== -->
|
||
|
||
|
||
<!-- =========== LEVEL_1_OUTPUT_RANKED_LIST_OF_SIMILAR_STRUCTURES =========== -->
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<A NAME="OutputRankedList"></A><A NAME="RankedList"></A>
|
||
|
||
<SPAN class="HeaderText3"><B>Ranked list of hits</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>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
The VAST+ <A HREF="#Output">search results</A> page lists all structures that were found to be similar in 3D shape to the query.<!-- {, as shown in the <I><A HREF="#OutputRankedListIllustration"><span style="color:#d70000">illustrated example</span></A></I> below.} --><BR><BR>
|
||
|
||
<!-- If desired, you can view only a subset of the search results by applying the <A HREF="#Filters">filters</A> described above. In addition, the search results page provides the following functions. Click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit. Click on this image to read more about the expanded view."> beside any structure to see a <A HREF="#GraphicalDisplays">[<A HREF="#QuerySubjectComparison">]detailed view/graphical display</A> comparing that structure to your query.<BR><BR -->
|
||
|
||
<A NAME="SortOrder"></A>
|
||
<A NAME="DefaultSortOrder"></A>
|
||
<B>Default sort order</B>: The similar structures are shown as a <B>ranked list</B>, based on the following <B>scores</B>:<BR>
|
||
(1) <A HREF="#SortOptionAlignedProteins">number of aligned proteins</A>, (2) <A HREF="#SortOptionRMSD">RMSD</A>, (3) <A HREF="#SortOptionAlignedResidues">number of aligned residues</A>, and (4) <A HREF="#SortOptionSequenceIdentity">sequence identity</A>, in that order.<BR>
|
||
It is also possible to sort by <A HREF="#SortOptionTaxonomy">taxonomy</A>, if desired.<BR><BR>
|
||
|
||
The blue arrow <IMG SRC="images/arrows_sort_order_blue_descending_grey_ascending.png" WIDTH="8" HEIGHT="15" BORDER="0" ALT="A blue arrow that appears to the right of the column header indicates the primary sort criterion. Downward pointing arrow indicates descending sort order, and upward pointing arrow indicates ascending order."> that appears to the <B>right</B> of the column header indicates the primary sort criterion, and the direction (ascending/descending) of the sort.<BR><BR>
|
||
|
||
<!-- A blue arrow <IMG SRC="images/arrow_bluedown_sort_order_descending.png" WIDTH="12" HEIGHT="11" BORDER="0" ALT="A blue arrow that appears to the right of the column header indicates the primary sort criterion. Downward pointing arrow indicates descending sort order, and upward pointing arrow indicates ascending order."> will appear to the <B>right</B> of the column header that you selected as the primary sort criterion, and will indicate the direction (ascending/descending) of the sort.<BR><BR -->
|
||
|
||
If desired, you can <B>override the default sort order</B> by <B>clicking</B> any arrow <IMG SRC="images/arrows_sort_order_grey_descending_grey_ascending.png" WIDTH="8" HEIGHT="15" BORDER="0" ALT="red arrow that appears to the right of the column header that is being used as the primary sort criterion. Downward pointing arrow indicates descending sort order, and upward pointing arrow indicates ascending order."> beside a <B>column header</B> in the output table in order to choose that column as the <B>primary sort criterion</B>. In that case, your selected criterion is applied first, and the remaining sort criteria applied afterward (in their usual order). The arrow beside the selected column header will turn blue, indicating it is now the primary sort criterion, and indicating the direction of the sort (ascending or descending).
|
||
|
||
<UL>
|
||
<BR>
|
||
|
||
<!-- =========== OUTPUT_SORT_OPTIONS =========== -->
|
||
|
||
<LI><A NAME="OutputSortOptions"></A><A NAME="SortOptions"></A><A NAME="Sort"></A><B>Sort Options (Scores)</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></LI><BR>
|
||
|
||
<OL>
|
||
|
||
<!-- LI><A NAME="SortOrder"></A><A NAME="SortDefault"></A><B>Default display and order of execution of sort options</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 text text text</LI><BR -->
|
||
|
||
<LI><A NAME="SortOptionAlignedProteins"></A><A NAME="AlignedProteins"></A><B>Aligned proteins</B> -- The number of protein molecules in the query structure have a match (i.e., similar 3D shape) to a protein molecule in the subject.</LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>If <B>all</B> of the molecules in the query structure match molecules in the subject, then a solid red circle icon <A HREF="#OutputFilterCompleteMatch"><IMG SRC="images/icon_red_circle_solid.png" WIDTH="12" HEIGHT="12" 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."></A> indicates there is a <A HREF="#OutputFilterCompleteMatch">complete match</A> to biological unit of query structure. <I>(<A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span> of VAST+ results</A>)</I></LI><BR>
|
||
|
||
<LI>If a <B>subset</B> of the molecules, or an <B>individual</B> molecule, from the query structure have matching molecules in the subject, then a half-filled red circle icon <A HREF="#OutputFilterPartialMatch"><IMG SRC="images/icon_red_circle_half_filled.png" WIDTH="12" HEIGHT="12" 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."></A> indicates there is a <A HREF="#OutputFilterPartialMatch">partial match</A> to biological unit of query structure. <I>(<A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span> of VAST+ results</A>)</I></LI><BR>
|
||
|
||
</UL>
|
||
|
||
|
||
<LI><A NAME="SortOptionRMSD"></A><A NAME="RMSD"></A><B>RMSD</B> -- The average root mean square deviation (RMSD), in Angstroms (Å), of all aligned residues between the query structure and the subject.</LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>This number is calculated after <B>optimal superposition</B> of two structures, as the square root of the mean square distances between equivalent C-alpha atoms. Smaller RMSD values indicate greater structural similarity. (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.)</LI><BR>
|
||
|
||
<LI>The <B>RMSD values</B> displayed in <A HREF="../vastplus.cgi">VAST+</A> results might be much <B>higher</B> than those displayed in <A HREF="#OriginalVAST">Original VAST</A> results because the 3D alignment is optimized for the whole assembly rather than for individual protein molecules. Specifically, VAST+ takes all of the individual 3D domain alignments and calculates a global superposition. To do this, individual protein molecules might be shifted from their ideal pairwise superposition, in order to be able to generate a global superposition of all matched molecules between the query structure and the subject.</LI><BR>
|
||
|
||
<LI>For example, <B>Original VAST</B> might give RMSD values of about <B>3-4 Å</B> at the worst, and rarely <B>up to 6 Å</B> for very large structures. In contrast, <B>VAST+</B> results might generate more hits with RMSD values of <B>5-6 Å</B> or more, and a number of cases with large values such as <B>20 Å or more</B>. This can be due to flexibility in the biological unit, which might indicate something interesting. An <B>example</B> is the chaperone protein <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=3J1B"><B>3J1B</B></A>: Cryo-em Structure of 8-fold Symmetric Ratcpn-alpha in APO State. The <A HREF="/Structure/vastplus/vastplus.cgi?uid=3J1B"><B>VAST+ neighbors for 3J1B</B></A> include <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=3J03">3J03</A>: Lidless Mm-cpn in the Closed State With Atpalfx, with an RMSD value of 13.41 Å.</LI><BR>
|
||
|
||
</UL>
|
||
|
||
|
||
<LI><A NAME="SortOptionAlignedResidues"></A><A NAME="AlignedResidues"></A><B>Aligned residues</B> -- The total number of amino acids, from all protein molecules in the query structure's biological unit, that are spatially aligned to the subject.</LI><BR>
|
||
|
||
<LI><A NAME="SortOptionSequenceIdentity"></A><A NAME="SequenceIdentity"></A><B>Sequence identity</B> -- The percent of aligned residues that are identical, averaged over all of the aligned protein molecules (rounded to the nearest whole number on the VAST+ results display).</LI><BR>
|
||
|
||
<LI><A NAME="SortOptionTaxonomy"></A><A NAME="Taxonomy"></A><B>Taxonomy</B> -- Click on the up/down arrows in the taxonomy header to sort hits alphabetically by genus name.<BR>
|
||
If you choose to sort by taxonomy, the similar structures are sorted based on the following criteria:<BR>
|
||
(1) alphabetically by genus, then within a genus, the structures are sorted based on (2) <A HREF="#SortOptionAlignedProteins">number of aligned proteins</A>, (3) <A HREF="#SortOptionRMSD">RMSD</A>, (4) <A HREF="#SortOptionAlignedResidues">number of aligned residues</A>, and (5) <A HREF="#SortOptionSequenceIdentity">sequence identity</A>, in that order.<BR>
|
||
<I>(Note: If you would like to only see the subset of search results from a specific superkingdom, use the <a href="#OutputFilterTaxonomy">taxonomy filter</a> to select the desired superkingdom, then click on the arrows in the "Taxonomy" column header of the search results table to sort the structures from the superkingdom alphabetically by genus.)</I></LI><BR>
|
||
|
||
</OL>
|
||
<BR>
|
||
|
||
<!-- =========== OUTPUT_VIEW_DETAILS_FOR_A_SIMILAR_STRUCTURE =========== -->
|
||
|
||
<LI><A NAME="OutputViewDetails"></A><B>View details for a similar 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></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>
|
||
|
||
Click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit. Click on this image to read more about the expanded view."> beside any structure to see a detailed view comparing the query structure to the matched structure. A separate section of this help document provides a <A HREF="#GraphicalDisplays"><!-- A HREF="#QuerySubjectComparison" -->description of the detailed view</A>. <!-- (The "Detailed Views/Graphical Displays" section of this document provides additional information about that display.) --></LI><BR>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<!-- =========== OUTPUT_SEARCH_WITHIN_RESULTS =========== -->
|
||
|
||
<LI><A NAME="OutputSearchWithinResults"></A><A NAME="SearchWithinResults"></A><B>Search within results</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></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>The "<B>Search within results</B>" text box enables you to <B>enter a PDB ID, MMDB ID, or text word from the title</B> of a structure of interest to find out if it among the similar structures retrieved by VAST, and if so, to instantly take you to the page of results on which it appears, with your structure of interest <B>highlighted</B> {in yellow}.<BR><BR>
|
||
|
||
If you are viewing only a <B>subset</B> of the search results (for example, because you have checked a box beside a bar graph of interest to filter the results), and your structure of interest is not in that subset but is in the overall search results, VAST will display a relevant message that includes a link which opens the complete set of search results, automatically highlighting your structure of interest.<BR><BR>
|
||
|
||
If, on the other hand, you enter a PDB ID of a structure that is <B>not</B> listed among the VAST results, you will see an error message indicating that your structure of interest was not among the results.</LI><BR><BR>
|
||
|
||
<LI><B>Example:</B> Retrieve the <A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB "><B>VAST results</B></A> for <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113"><B>1HBB</B></A>: "High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site (human hemoglobin)." Let's say that you suspect <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=66087"><B>1UMO</B></A> ("The Crystal Structure Of Cytoglobin: The Fourth Globin Type Discovered In Man") will be one of the structures retrieve and you quickly want to find where that structure falls within the ranked list of similar structures. To do that, simply enter the PDB ID 1UMO (or its corresponding MMDB ID 66087) in the "search within results" text box, and you will be taken immediately to the appropriate page of search results, with 1UMO <SPAN style="background-color: #FFFF00">highlighted in yellow</SPAN>. You can then click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit."> to the left of that structure in order to see more details about the comparison between 1HBB and 1UMO. If you enter the PDB ID or MMDB ID of a structure that is not similar (as determined by VAST+) to the query structure, a pop-up message will appear that says, "XXX is not a simlar structure of 1HBB."</LI>
|
||
|
||
</UL>
|
||
|
||
<!-- =========== OUTPUT_SAVE =========== -->
|
||
|
||
<!-- LI><A NAME="OutputSave"></A><B>Save search results as CSV file</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></LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR -->
|
||
|
||
<!-- =========== OUTPUT_ORIGINAL_VAST_BUTTON =========== -->
|
||
|
||
<!-- LI>
|
||
<A NAME="OriginalVASTButton"></A>
|
||
|
||
<A NAME="OutputOriginalVASTButton"></A><B>"Original VAST" button</B> (on the search results page) <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><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>The "Original VAST" button gives you the option to view your search results in the original style VAST display, which lists structures that have similarities to <B>individual protein molecules</B> in your query structure, and allows you to view their sequence alignments and 3D superpositions. (An <I><A HREF="#OriginalVastDisplay"><SPAN style="color:#D70000">illustrated example</SPAN></A></I> of the original-style VAST results is provided in the Graphical Displays section of this document.)<BR><BR>
|
||
|
||
(In contrast, the new VAST+ search results rank similar structures based on their <A HREF="#OutputBiologicalUnit">biological unit</A> similarity to the query structure, and provide the ability to view sequence alignments and superpositions of the biological units.)</LI><BR><BR>
|
||
|
||
</UL>
|
||
<BR -->
|
||
|
||
<!-- ====== OUTPUT_NULL_RESULTS_NO_MATCHED_STRUCTURE_FOUND ======== -->
|
||
|
||
<!-- LI><A NAME="NullResult"></A><A NAME="NoNeighborFound"></A><A NAME="NoMatchedStructureFound"></A><A NAME="OutputNoMatchedStructureFound"></A>
|
||
<B>Null result: "No matched structure found"</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>
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" border="1">
|
||
<TR>
|
||
<TD>TABLE data cell 1</TD>
|
||
<TD>TABLE data cell 2</TD>
|
||
<TD>TABLE data cell 3</TD>
|
||
</TR>
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
</LI><BR><BR -->
|
||
|
||
<!-- =========== OUTPUT_NEW_SEARCH_BUTTON =========== -->
|
||
|
||
<!-- LI><A NAME="OutputNewSearchButton"></A><B>"New Search" button</B> (on the search results page)<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><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR -->
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- ======== END_LEVEL_1_OUTPUT_RANKED_LIST_OF_SIMILAR_STRUCTURES ========== -->
|
||
|
||
|
||
<!-- ========== LEVEL_1_OUTPUT_ORIGINAL_VAST_BUTTON ============ -->
|
||
|
||
<A NAME="OriginalVASTButton"></A>
|
||
<A NAME="OutputOriginalVASTButton"></A>
|
||
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>"Original VAST" button</B></SPAN> (on the search results page) <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>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
An "Original VAST" button is located near the top of a VAST+ search results page<!--, on the right-hand end of the grey "Similar Structures" header bar. -->It gives you the option to view your search results in the original style VAST display, which lists structures that have similarities to <B>individual protein molecules</B> or <B>individual</B> <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains"><B>3D domains</B></A> in your query structure, and allows you to view their sequence alignments and 3D superpositions. An <A HREF="#OriginalVastDisplay"><SPAN style="color:#D70000"><I>illustrated example</I></SPAN> of the original-style VAST results</A> is provided in the Graphical Displays section of this document.<BR><BR>
|
||
|
||
<I>(In contrast, the new VAST+ search results rank similar structures based on their <A HREF="#OutputBiologicalUnit">biological unit</A> similarity to the query structure (<A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span> of VAST+ results</A>), and provide the ability to view sequence alignments and superpositions of the biological units)</I><BR><BR>
|
||
|
||
A separate section of this document describes the <A HREF="#Compare"><B>difference between Original VAST and VAST+</B></A>.<BR><BR>
|
||
|
||
<!-- An <A HREF="#OriginalVASTDisplay"><SPAN style="color:#D70000">illustrated example</SPAN></A> of the original-style VAST results is provided in the <A HREF="#GraphicalDisplays">Graphical Displays</A> section of this document. Or, to compare the views directly, you can:<BR>
|
||
|
||
- <A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB">open a live web page with <B>VAST+ results</B> for 1HBB</A><BR>
|
||
|
||
[- <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113&ShowOp=VastSum">open a live web page with <B>original-style VAST results</B> for 1HBB</A><BR>]
|
||
|
||
- <A HREF="/Structure/vastplus/vastplus.cgi?uid=1HBB&style=old">open a live web page with <B>original-style VAST results</B> for 1HBB</A><BR>
|
||
|
||
<I>Tip: Right click on each link above and select "open in new window" in order to be able to compare the views side by side. This help document explains the features and functions of the [<A HREF="../vastplus/vastplus.cgi">]VAST+ results page, and the <A HREF="../../VAST/vasthelp.html">original VAST help document</A> explains the features and functions of the original VAST results page.</I -->
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
|
||
<!-- ========= END_LEVEL_1_OUTPUT_ORIGINAL_VAST_RESULTS_DISPLAY =========== -->
|
||
|
||
<!-- ====== LEVEL_1_OUTPUT_NULL_RESULT_NO_MATCHED_STRUCTURE_FOUND ======= -->
|
||
|
||
<A NAME="NullResult"></A>
|
||
<A NAME="NoNeighborFound"></A>
|
||
<A NAME="NoMatchedStructureFound"></A>
|
||
<A NAME="OutputNoMatchedStructureFound"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>"No matched structure found" (null result)</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>
|
||
|
||
VAST+ results are available for most, but not all, structures. If your query generates the message, "<B>No matched structure found</B>," it can be for one of the reasons listed in the table below. If your query does not have VAST+ neighbors, but does have <A HREF="#OriginalVAST">Original VAST</A> neighbors, follow the link provided in the error message to view the available results. If your query structure is relatively new, try your search again at a later date, as VAST (and VAST+) neighbors are calculated/updated weekly.
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ========== 2_COLUMN_TABLE_NULL_RESULTS =============== -->
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" border="black 1px" cellpadding="4" class="format1 TableText1">
|
||
|
||
<!-- ===== NULL_RESULT_CATEGORY_1_NO_VAST+_OR_ORIGINAL_VAST_NEIGHBORS ======= -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" align="center" style="white-space: nowrap;" colspan="2"><A NAME="NullResultForVASTplusAndVAST"></A>Circumstances under which a structure has <B>neither</B> VAST+ nor Original VAST results:</TD>
|
||
</TR>
|
||
|
||
<!-- ============= NULL_RESULT_TOO_NEW ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResultTooNew"></A>VAST neighbors not yet calculated<!-- structure is too new --></TD>
|
||
<TD class="format1A" valign="top">VAST neighbors are currently being calculated for your query structure and are therefore not yet available. Try your search again in several days, as VAST (and VAST+) neighbors are calculated/updated on a weekly basis.<!-- Structure is new and has not yet been neighbored by VAST. --></TD>
|
||
</TR>
|
||
|
||
<!-- ============= NULL_RESULT_TOO_SMALL ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResultTooSmall"></A>structure is too small</TD>
|
||
<TD class="format1A" valign="top">In order to be processed by VAST, a protein molecule must have at least three secondary structure elements (alpha helices and/or beta sheets). If an individual protein in a structure contains only one or two secondary structure elements, that protein will not be processed by VAST. Structures that are composed entirely of such proteins will therefore have no VAST neighbors.<!-- Structure has not and will not be neighbored by VAST (no polypeptide chains that qualify for structure neighboring). --></TD>
|
||
</TR>
|
||
|
||
<!-- ============= NULL_RESULT_NO_PROTEIN ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResultNoProtein"></A>structure has no protein</TD>
|
||
<TD class="format1A" valign="top">Currently, VAST works only on protein molecules. If a structure does not contain any proteins, for example, if it contains only DNA or RNA molecules, it will not be processed by VAST, and will therefore have no VAST neighbors.<!-- Structure has not and will not be neighbored by VAST (no polypeptide chains that qualify for structure neighboring). --></TD>
|
||
</TR>
|
||
|
||
<!-- ============= NULL_RESULT_UNIQUE_STRUCTURE ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResultUniqueStructure"></A>structure is unique</TD>
|
||
<TD class="format1A" valign="top">The structure is large enough to be processed by VAST+ (i.e., has at least three secondary structure elements), but has a unique 3D shape which has not been found among any of the other publicly available structures.<!-- Structure has been neighbored but did not generate any VAST results (polypeptide chains may be too short or too unique). --></TD>
|
||
</TR>
|
||
|
||
<!-- === NULL_RESULT_CATEGORY_2_NO_VAST+_but_has_ORIGINAL_VAST_NEIGHBORS ==== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" align="center" style="white-space: nowrap;" colspan="2"><A NAME="NullResultForVASTplusOnly"></A>Circumstances under which a structure has <B>no VAST+</B> results, but <B>does have Original VAST</B> results:</TD>
|
||
</TR>
|
||
|
||
<!-- ============= NULL_RESULT_TOO_NEW_LAG_TIME_FOR_VAST+ ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResultTooNewVASTplusLagTime"></A>VAST+ neighbors not yet calculated<!-- structure is too new --></TD>
|
||
<TD class="format1A" valign="top">VAST+ neighbors are currently being calculated for your query structure and are therefore not yet available. As noted in the <A HREF="#WhatIs">overview</A> section of this document, the VAST+ is an extension of, and built upon, the original VAST system. Therefore, there may be some lag between the availability of original VAST data and the subsequent appearance of VAST+ data in the system.<!-- (VAST+ is an extension of, and built upon, the original VAST system. Therefore, Original VAST neighbors are generally available before the VAST+ neighbors.) --> Try your search again in several days, as VAST (and VAST+) neighbors are calculated/updated on a weekly basis.
|
||
<!-- Structure is new and has not yet been neighbored by VAST. --></TD>
|
||
</TR>
|
||
|
||
<!-- ============= NULL_RESULT_NO_BIOLOGICAL_UNIT ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResultNoBiologicalUnit"></A>structure has no biological unit defined</TD>
|
||
<TD class="format1A" valign="top">If a structure record does not have a <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A> defined in its source PDB file, it is only available as an <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingAsymmetricUnit">asymmetric unit</A> (i.e., raw structure data). In that case, the structure is not processed by VAST+, since VAST+ focuses on finding similarities among biological units. However, such structures are processed by the <A HREF="#OriginalVAST">Original VAST</A> algorithm, which may have found structures that are geometrically similar to individual proteins, or individual <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domains</A>, in your query structure.<!-- However, that structure might have original VAST neighbors, which are geometrically similar to individual proteins in the structure. In that case, view the original VAST results for your query structure. --></TD>
|
||
</TR>
|
||
|
||
<!-- ============= NULL_RESULT_MERGED_STRUCTURE ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResultMergedStructure"></A>merged structure</TD>
|
||
<TD class="format1A" valign="top"><A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingMergeSplitFiles">Merged structures</A>, which have been assembled from PDB split files, do not have a biological unit defined, and are therefore not processed by VAST+. However, such structures are processed by the original VAST algorithm, which may have found structures that are geometrically similar to individual proteins in your query structure. In that case, view the original VAST results for your query structure.</TD>
|
||
</TR>
|
||
|
||
<!-- ============= NULL_RESULT_TOO_LARGE ============== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResultTooLarge"></A>structure is too large</TD>
|
||
<TD class="format1A" valign="top">Structures that have biological units composed of 60 or more protein molecules are not currently processed by VAST+. However, such structures are processed by the original VAST algorithm, which may have found structures that are geometrically similar to individual proteins in your query structure. In that case, view the original VAST results for your query structure.</TD>
|
||
</TR>
|
||
|
||
<!-- ========= NULL_RESULT_NO_FULL_LENGTH_PROTEIN_NEIGHBOR =========== -->
|
||
|
||
<TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResultNoFullLengthProteinMatch"></A><A NAME="FullLengthProtein"></A><A NAME="FullLengthProteinMatch"></A>structure has no full length<BR>protein neighbor</TD>
|
||
<TD class="format1A" valign="top">The structure has been neighbored by VAST, but did not generate VAST results for the any full-length protein molecule in the query, so the structure has not been considered for VAST+.<BR><BR>
|
||
VAST+ results only list structures that have a complete match or partial match to your query structure's biological unit, or have a match to at least one full protein molecule in the query structure.<!-- {A protein match is considered to be full length if it covers __% of the span of amino acids that are spatially aligned, and if at least three secondary structure elements are aligned.} --><BR><BR>
|
||
Even if no full length protein matches are found, the query structure might still have hits in Original VAST, because it is still possible that a portion of a protein in the query structure, or an individual 3D domain, has a match to another structure. In that case, view the original VAST results for your query structure.<!-- Structure has been neighbored by VAST, but did not generate any VAST results for the <20>full-length chain<69> query, hence it has not been considered for VAST+ --></TD>
|
||
</TR>
|
||
|
||
<!-- ============= XXXXXX_NO_UP_ARROW ============== -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResult______"></A>______Column1__________</TD>
|
||
<TD class="format1A" valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= XXXXXX_WITH_UP_ARROW ============== -->
|
||
|
||
<!-- TR>
|
||
<TD class="format1H" valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="NullResult______"></A>______Column1__________</TD>
|
||
<TD class="format1B" valign="top">
|
||
<A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></IMG></A>
|
||
______Column2__________<BR><BR>
|
||
</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_2_COLUMN_TABLE ================ -->
|
||
|
||
<!-- ====== END_LEVEL_1_OUTPUT_NULL_RESULT_NO_MATCHED_STRUCTURE_FOUND ====== -->
|
||
|
||
<!-- ============== LEVEL_1_OUTPUT_NEW_SEARCH ================ -->
|
||
|
||
<A NAME="NewSearch"></A>
|
||
<A NAME="OutputNewSearch"></A>
|
||
<A NAME="OutputNewSearchButton"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>"New Search" button</B></SPAN> (on the search results page) <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>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
To retrieve the VAST+ results for a different structure, simply enter its <A HREF="#OutputPDBID">PDB ID</A> or <A HREF="#OutputMMDBID">MMDB ID</A> in the text box in the upper right hand corner of a VAST+ results page and press the "<B>New Search</B>" button. Or, enter either ID on the <A HREF="../vastplus.cgi">VAST+</A> query page.
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- =============== END_LEVEL_1_OUTPUT_NEW_SEARCH =============== -->
|
||
|
||
<!-- ====== 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 MiniText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ########### BLUE_HEADER_SECTION_5_GRAPHICAL_DISPLAYS ############# -->
|
||
|
||
<A NAME="DetailedView"></A>
|
||
<A NAME="GraphicalDisplays"></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">Detailed Views/Graphical Displays for Individual Hits</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_GRAPHICAL_DISPLAYS ############ -->
|
||
|
||
|
||
<!-- ########## 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_THIS_SECTION ============== -->
|
||
<BR>
|
||
<BLOCKQUOTE>
|
||
|
||
<A HREF="#QuerySubjectComparison">detailed view comparing the query structure and a matched structure</A> | <A HREF="#SeqAlignView">sequence alignment views</A> | <A HREF="#3DView">3D views</A> | <A HREF="#OriginalVASTDisplay">original style VAST display</A>
|
||
|
||
</BLOCKQUOTE>
|
||
<BR>
|
||
|
||
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
||
|
||
<!-- ============== LEVEL_1_QUERY_VS_SUBJECT_COMPARISON ================ -->
|
||
|
||
<A NAME="QuerySubjectComparison"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Detailed View Comparing the Query Structure and a Matched 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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
The VAST+ <A HREF="#Output">search results</A> page provides a concise list of the structures that are similar in 3D shape to your query structure, listing the PDB ID and description of each one, along with statistical information for the match.
|
||
<SPAN style="background-color: #FFFF00"><B>Click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit."></SPAN> beside any structure</B> to see a detailed view/graphical display comparing the query structure to the matched structure.<BR><BR>
|
||
|
||
Each of the <I><A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span></A></I> of VAST+ search results<!-- for <A HREF="#IllustratedExample1B26">1B26 (Glutamate Dehydrogenase, <I>Thermotoga maritima</I>)</A> and <A HREF="#IllustratedExample1HBB">1HBB (Deoxyhemoglobin, <I>Homo sapiens</I>)</A --> features a detailed view for one of the matched structures:<BR>
|
||
<A HREF="#IllustratedExample1B26"><B>IB26</B> (Glutamate Dehydrogenase, <I>Thermotoga maritima</I> vs. <B>1GTM</B> (Glutamate Dehydrogenase, <I>Pyrococcus furiosus</I>)</A><BR>
|
||
<A HREF="#IllustratedExample1HBB"><B>1HBB</B> (Deoxhemoglobin, <I>Homo sapiens</I>) vs. <B>1FSL</B> (Leghemoglobin, <I>Glycine max</I>)</A>.<BR><BR>
|
||
|
||
The detailed view includes:
|
||
<!-- For additional details about any hit, click on the plus (+) beside the structure of interest. That will open a detailed view/graphical display comparing the selected structure to your query, which includes: --><BR><BR>
|
||
|
||
<A NAME="AlignedMolecules"></A><B>Aligned Molecules</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>
|
||
|
||
The detailed view of a VAST+ hit shows a table of "<B>Aligned Molecules</B>," which provides a graphical overview of the extent of the 3D similarity between the query structure and the matched structure (i.e., the VAST+ "neighbor"). It includes a clickable <A HREF="#OutputInteractionsSchematic">interaction schematic</A> for each structure, and a clickable list of matching proteins, as described below.<BR><BR>
|
||
|
||
The <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMMDBID">MMDB ID</A> for each structure links to the corresponding <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">MMDB summary page</A>, which provides additional details about the structure's molecular components (proteins, nucleotides, chemicals), links to associated publications, and more. The summary page also provides a "<A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvStructureView">View structure</A>" link that opens an interactive 3D view of the <B>individual structure</B>.
|
||
|
||
To view a 3D <B>superposition</B> of the query structure and the matched structure, click the "<A HREF="#3DViews">Visualize 3D structure superposition with Cn3D</A>" button beneath the lists of Aligned Molecules.
|
||
|
||
In either case, NCBI's free <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> program (version 4.3.1 or later) must be installed on your computer and configured as a helper application for your browser in order for the "View structure" or "Visualize 3D structure superposition with Cn3D" buttons to open the 3D view.
|
||
|
||
<!-- Whether you press the "View structure" or "Visualize 3D structure superposition with Cn3D" button, NCBI's free <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> program (version 4.3.1 or later) must be installed on your computer and configured as a helper application for your browser in order for the buttons to open the 3D structure. --><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="QuerySubjectComparisonInteractionsSchematic"></A><B>Interaction schematic of query structure vs. matched 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></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>The <A HREF="#OutputInteractionsSchematic">interaction schematics</A> for both the <B>query structure</B> and the <B>matched structure</B> (VAST+ neighbor) are displayed side by side. Protein molecules that have a match are designated by a <B>broken (dashed) outline</B>. Protein molecules that do not have a match are shown with a <B>solid outline</B>. <B>Click on the icon of any protein molecule</B> in either one of the interaction schematics to see the protein's name and to highlight the corresponding molecule in the other structure. When you click on an icon, its <B>broken (dashed) outline</B> will change from <B>red to black</B>, and its <B>protein name</B> will be <B>highlighted in yellow</B>. The matching protein in the other structure will be highlighted in the same way.<BR><BR>
|
||
|
||
|
||
<A NAME="SelectedProtein"></A><A NAME="SelectedMolecule"></A><A NAME=" QuerySubjectComparisonSelectedProtein"></A>The molecule that is highlighted in the query structure's <A HREF="#OutputInteractionsSchematic">interaction schematic</A> and protein list is referred to as the <SPAN style="background-color: #FFFF00"><B>selected protein</B></SPAN>, and is the focal point of the 3D and sequence alignment displays. For example, if you select a protein from the query structure and then press the button for "<A HREF="#3DViews">Visualize 3D structure superposition (with Cn3D app)</A>" or "<A HREF="#SeqAlignViews">View aligned sequences</A>," the 3D view and sequence alignment windows will be centered on the selected protein. You can then rotate the 3D view and scroll through the sequence alignment window to see other proteins, if desired, but the initial view will be centered on the selected protein.<!-- {check to see if the selected protein is also the focal point when a structure is opened in iCn3D} --><BR><BR>
|
||
|
||
<!-- I>(Note: An earlier section of the help document provides <A HREF="#OutputInteractionsSchematic">additional details about the interaction schematic</A>, including a description of the icons used to represent the protein, nucleotide, and chemical components of a structure.)</I -->
|
||
|
||
</LI><BR>
|
||
|
||
</UL>
|
||
|
||
<LI><A NAME="QuerySubjectComparisonProteinList"></A><B>List of matching protein molecules</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></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>Beside each interaction schematic is a <B>list of the proteins</B> that are spatially aligned to a protein in the matching structure. <B>Click on the name of any protein</B> to highlight that protein in both the list and in the interaction schematic. This action will also automatically highlight the name and icon of the matching protein in the other structure.<BR><BR>
|
||
|
||
Regardless of how many proteins are present in the biological unit of the query structure or subject, the list of protein names shows only the <B>subset of proteins that have 3D similarity to each other</B>. (You can still see the names of other proteins in the query or subject, however, by clicking on the icons in the interaction schematics.)</LI><BR>
|
||
|
||
<!-- LI><A NAME="_____________"></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 text text text</LI><BR -->
|
||
|
||
</UL>
|
||
|
||
<!-- LI><A NAME="QuerySubjectComparisonMoleculeGraphic"></A><A NAME="MatchedBiounit"></A><B>Matched Biological Unit [Molecular graphic of subject]</B></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>The 3D molecular graphic shows a single static snapshot of the matched structure's 3D shape, generated by the <A HREF="/Structure/CN3D/cn3d.shtml">Cn3D</A> program. In general, it shows the default [<A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms">]<A HREF="#OutputBiologicalUnit">biological unit</A> of the structure.[<I>(See the MMDB help document for <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvThumbnailMolecularGraphic">additional information</A> about molecular graphic thumbnail images.)</I>]<BR><BR>
|
||
To view the 3D structure interactively, click on its MMDB ID. That will open the corresponding <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">structure summary</A> page in MMDB, where you can choose to "View structure." The structure summary page will also provide additional details about the structure's molecular components (proteins, nucleotides, chemicals).<BR><BR>
|
||
To view a 3D superposition of the subject and the query structure, click the "<A HREF="#3DView">3D View</A>" button beside any protein pair in the list of matching protein molecules.<BR><BR>
|
||
In either case, NCBI's free <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> program must be installed on your computer and configured as a helper application for your browser in order for the "View structure" or "3D View" buttons to open the 3D structure.</LI><BR>
|
||
|
||
</UL>
|
||
<BR -->
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- =============== END_LEVEL_1_QUERY_VS_SUBJECT_COMPARISON =============== -->
|
||
|
||
|
||
<!-- ============== LEVEL_1_SEQUENCE_ALIGNMENT_VIEWS ================ -->
|
||
|
||
<A NAME="SeqAlignView"></A>
|
||
<A NAME="SeqAlignViews"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Sequence Alignment Views</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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<UL>
|
||
|
||
<LI>VAST does two things for each pair of similar proteins: it calculates an optimal 3D superposition for the conserved core, and constructs a <B>sequence alignment based on the correlation of the 3D structures</B>.</LI><BR>
|
||
|
||
<LI>The <a HREF="#QuerySubjectComparison">detailed view</A> of a query vs. subject structure comparison (which opens when you click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit."> beside any hit) allows you to view the pairwise sequence alignments of matching protein pairs. To do this, click on the "<B>View aligned sequences</B>" button that appears beneath the list of matching protein molecules. A separate window will open, showing the pairwise sequence alignments for all matching protein molecules. If you <A HREF="#SelectedProtein">selected a protein</A> from the query structure's interaction schematic or protein list before pressing the "View aligned sequences" button, the sequence alignment display will automatically scroll to the selected protein.</LI><BR>
|
||
|
||
<LI>The sequence alignments shown in VAST use the following conventions:</LI><BR>
|
||
<UL>
|
||
<LI><B>UPPER CASE LETTERS</B> represent <B>amino acids that are aligned in 3D space,</B></LI>
|
||
<LI><B>LOWER CASE LETTERS</B> represent <B>unaligned amino acids</B>, and</LI>
|
||
<LI><B><span style="color:#d70000">RED LETTERS</span></B> represent <B>identical amino acids</B>.</LI>
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI>Because the protein alignments produced by VAST do not require sequence similarity (but instead simply require a common spatial position of amino acids), these views do not necessarily represent alignments of evolutionarily conserved sequence blocks. However, the 3D alignments often coincide with evolutionarily conserved sequence blocks.
|
||
<!-- Therefore, the sequence alignments shown in VAST reflect a common spatial position of each pair of amino acids that are shown in <B>UPPER CASE LETTERS</B>, and not necessarily alignments of evolutionarily conserved sequence blocks (although conserved sequence blocks often coincide with the 3D alignments, sequence similarity is not required for the protein alignments produced by VAST). In other words, the upper case letters represent <B>amino acids that are aligned in 3D space</B>. The <B>LOWER CASE LETTERS</B> represent <B>unaligned amino acids</B>. <B><span style="color:#d70000">RED LETTERS</span></B> represent identical amino acids.<BR><BR --></LI><BR>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ======= BOXED_NOTE_OUTPUT_SEQUENCE_ALIGNMENT_ILLUSTRATED_EXAMPLE ======= -->
|
||
|
||
<A NAME="SeqAlignViewIllustration"></A>
|
||
<A NAME="SeqAlignViewsIllustration"></A>
|
||
<!-- {TABLE width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell" ALIGN="Center" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="10" class="WhiteCell NormalText3">
|
||
<TR>
|
||
<TD class="WhiteCell" WIDTH="40" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
<TD class="WhiteCellBlueEdgeAll" ALIGN="Left" VALIGN="TOP">
|
||
<P class="indent20bottomspace NormalText3"><P class="pad10"><B>Example</B> - Sequence alignment (08 November 2013) of<BR>
|
||
<B>____protein_name____</B> from <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113"><B>1HBB</B></A><BR>High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site:<BR>
|
||
<B>Vs.</B><BR>
|
||
<B>____protein_name____</B> from
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=____"><B>____</B></A><BR>__________title_of_structure________________<BR><BR>
|
||
<IMG SRC="images/______" WIDTH="600" HEIGHT="200" BORDER="0" ALT="________"><BR>
|
||
[<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113&ShowOp=VastSum">Open a live web page with original-style VAST results for 1HBB</A>]</P>
|
||
</TD>
|
||
<TD class="WhiteCell" WIDTH="40" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR} -->
|
||
|
||
<!-- ======= END_BOXED_NOTE_OUTPUT_SEQUENCE_ALIGNMENT_ILLUSTRATED_EXAMPLE ======= -->
|
||
|
||
<!-- =============== END_LEVEL_1_SEQUENCE_ALIGNMENT_VIEWS =============== -->
|
||
|
||
|
||
<!-- ============== LEVEL_1_3D_VIEWS ================ -->
|
||
|
||
<A NAME="3DView"></A>
|
||
<A NAME="3DViews"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>3D Views</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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<UL>
|
||
|
||
<!-- LI><A NAME="3DViewQuery"></A><B>Query structure 3D view</B></LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR -->
|
||
|
||
|
||
<!-- LI><A NAME="3DViewSubject"></A><B>Similar structure (VAST neighbor) 3D view</B></LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR -->
|
||
|
||
|
||
<LI><A NAME="3DViewSuperposition"></A><B>Superposition of query and similar structure in 3D</B></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>The <a HREF="#QuerySubjectComparison">detailed view</A> of a query vs. subject structure comparison (which opens when you click on the <B>plus button</B> <IMG SRC="images/button_expand_plus.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="The Plus button, which expands the view of a structure neighbor so you can view the details of the match betwen your query structure and the hit."> beside any hit) provides a "<B>Visualize 3D structure superposition</B>" button at the bottom of the table of aligned molecules. That button opens a menu that allows you to <B>choose which program to use</B> for interactively viewing the superposition:<BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="3DViewSuperpositioniCn3D"></A><A NAME="iCn3D"></A><A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D (Web)</B></A> - NCBI's WebGL-based viewer that provides interactive views of macromolecular structures and chemicals without the need to install a separate application.</LI><BR>
|
||
<UL>
|
||
<LI>Note: To use iCn3D, you just need to use a <B><I>web browser that supports <A HREF="https://get.webgl.org/">WebGL</A></I></B>. If your browser doesn't support WebGL, you might need to modify the settings in the browser to enable WebGL, or 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><BR>
|
||
<LI><B>iCn3D's 3D view window</B> will show the complete biological unit of the query structure and its VAST+ neighbor.</LI><BR>
|
||
<LI>Click on <B>iCn3D's "View Sequence"</B> button, if desired, to open a <B>sequence view window</B> that shows all pairs of aligned sequences from the query structure and its VAST+ neighbor.</LI><BR>
|
||
<LI>Note that iCn3D can show two different types of 3D superpositions: (1) <A HREF="#AlgorithmAlignmentInitial">initial alignment</A>, in which all matching molecules are superposed, and (2) <A HREF="#AlgorithmAlignmentRefined">refined alignment</A>, in which an invariant substructure is superposed).</LI>
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="3DViewSuperpositionCn3D"></A><A NAME="Cn3D"></A><A HREF="../../CN3D/cn3d.shtml"><B>Cn3D (App)</B></A> - a helper application for your web browser, available for Windows and Macintosh, which simultaneously displays structure, sequence, and alignment, and has powerful annotation and alignment editing features</LI><BR>
|
||
<UL>
|
||
<LI>Note: In order for this selection to work, you must have <A HREF="../../CN3D/cn3d.shtml">Cn3D 4.3.1</A> installed on your computer.</LI><BR>
|
||
<!-- LI>In order for the "Visualize 3D structure superposition" button to work, you must have <A HREF="../../CN3D/cn3d.shtml">Cn3D 4.3.1</A> installed on your computer; see important note below.</LI -->
|
||
<!-- LI>Note: if you choose Cn3D, you must install the most recent version of the program, <A HREF="../../CN3D/cn3d.shtml">Cn3D 4.3.1</A>, in order to view the superpositions of all matching molecules in the query and subject.</LI><BR -->
|
||
<LI><B>Cn3D's 3D view window</B> will show the complete biological unit of the query structure and its VAST+ neighbor. The 3D view will be centered on the <A HREF="#SelectedProtein">selected protein</A> (i.e., on the protein that was highlighted in the <A HREF="#QuerySubjectComparisonInteractionsSchematic">query structure's interaction schematic</A> before you pressed the "Visualize 3D structure superposition" button)</LI><BR>
|
||
<LI><B>Cn3D's "Sequence/Alignment Viewer" window</B> will open automatically, showing the <A HREF="#SelectedProtein">selected protein</A> that you chose in the <A HREF="#QuerySubjectComparisonInteractionsSchematic">query structure's interaction schematic</A> (or showing structure's first pair of aligned sequences from the query structure and its VAST+ neighbor, if you didn't click on any protein in the interactions schematic).<BR>
|
||
To view a different pair of aligned sequences, you can either:</LI>
|
||
<UL>
|
||
<LI>go back to the VAST+ search results page and click on the protein of interest in the query structure's interaction schematic (and then follow the options again to "Visualize 3D structure superposition > Cn3D (app)" or</LI>
|
||
<LI> choose the "Select > Pick Structures" menu option in Cn3D and then use CTRL+Click in the list of proteins to select the new protein you'd like to see in the "Sequence/Alignment Viewer" window.</LI>
|
||
</UL>
|
||
|
||
<!-- LI>The 3D view will be centered on the <A HREF="#SelectedProtein">selected protein</A> (i.e., on the protein that was highlighted in the <A HREF="#QuerySubjectComparisonInteractionsSchematic">query structure's interaction schematic</A> before you pressed the "Visualize 3D structure superposition" button), and its sequence data featured in the Cn3D's sequence alignment window.</LI -->
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
</UL>
|
||
|
||
<LI>The <a HREF="#OutputFolderTabs"><B>folder tabs</B></A> on the VAST+ search results page affect which type of alignment will be shown in the 3D view.<BR>
|
||
For example, when you click on the "Visualize 3D structure superposition" button, you will either see:<BR><BR>
|
||
<UL>
|
||
<LI>all matching molecules superposed (initial alignment)<BR>OR<BR></LI>
|
||
<LI>invariant substructure superposed (refined alignment),</LI>
|
||
</UL>
|
||
<BR>
|
||
depending on which folder tab you have selected.<BR><BR>
|
||
The <A HREF="#Algorithm">VAST algorithm</A> section of this document provides more details about the <A HREF="#AlgorithmAlignmentInitial">initial alignment</A> and <A HREF="#AlgorithmAlignmentRefined">refined alignment</A>, as well as an example of each.
|
||
</LI><BR>
|
||
|
||
<!-- LI><A NAME="_____________"></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 text text text</LI><BR -->
|
||
|
||
</UL>
|
||
|
||
<!-- LI><B>Important note: Cn3D version for viewing VAST+ superpositions:</B></LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>In order to view the superpositions of all matching molecules in the query and subject, you must install the most recent version of the NCBI molecular viewing software, <A HREF="../../CN3D/cn3d.shtml">Cn3D 4.3.1</A>.</LI><BR>
|
||
|
||
</UL>
|
||
<BR -->
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ======= BOXED_NOTE_OUTPUT_3D_SUPERPOSITION_ILLUSTRATED_EXAMPLE ======= -->
|
||
|
||
<A NAME="3DViewSuperpositionIllustration"></A>
|
||
<!-- {TABLE width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell" ALIGN="Center" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="10" class="WhiteCell NormalText3">
|
||
<TR>
|
||
<TD class="WhiteCell" WIDTH="40" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
<TD class="WhiteCellBlueEdgeAll" ALIGN="Left" VALIGN="TOP">
|
||
<P class="indent20bottomspace NormalText3"><P class="pad10">{<B>Example</B> - 3D superposition (10 July 2013) of<BR>
|
||
<B>____protein_name____</B> from <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113"><B>1HBB</B></A><BR>High-resolution X-ray Study of Deoxyhemoglobin Rothschild 37beta Trp-> Arg: a Mutation That Creates an Intersubunit Chloride-binding Site:<BR>
|
||
<B>with</B><BR>
|
||
<B>____protein_name____</B> from
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=____"><B>____</B></A><BR>__________title_of_structure________________<BR><BR>
|
||
<IMG SRC="images/______" WIDTH="600" HEIGHT="200" BORDER="0" ALT="________"><BR>
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1113&ShowOp=VastSum">Open a live web page with original-style VAST results for 1HBB</A>}</P>
|
||
</TD>
|
||
<TD class="WhiteCell" WIDTH="40" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR} -->
|
||
|
||
<!-- ======= END_BOXED_NOTE_OUTPUT_3D_SUPERPOSITION_ILLUSTRATED_EXAMPLE ======= -->
|
||
|
||
<!-- =============== END_LEVEL_1_3D_VIEWS =============== -->
|
||
|
||
<!-- ==== LEVEL_1_GRAPHICAL_DISPLAYS_ORIGINAL_VAST_ILLUSTRATED_EXAMPLE ==== -->
|
||
|
||
<A NAME="OriginalVAST"></A>
|
||
<A NAME="OutputOriginalVAST"></A>
|
||
<A NAME="OriginalVASTDisplay"></A>
|
||
<A NAME="OriginalVastDisplay"></A>
|
||
<A NAME="OutputOriginalVASTDisplay"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Original style VAST display</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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
The <B>original style VAST display</B>:
|
||
|
||
<UL>
|
||
|
||
<LI>lists each <!-- A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents"><A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvProteins" --><B>protein molecule</B> and <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains"><B>3D domain</B></A> in the <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingAsymmetricUnit"><B>asymmetric unit</B></A> of the query structure<!-- lists the protein molecules ("chains") in the query structure and the <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domains</A> that were identified in each protein -->, and</LI><BR>
|
||
|
||
<LI>retrieves structures that are similar in shape to any <B><I>individual</I> protein molecule or 3D domain</B>, and enables you to view their sequence alignments and 3D superpositions.</LI>
|
||
|
||
</UL>
|
||
|
||
<!-- BLOCKQUOTE><I>(In contrast, the newer <A HREF="#Output"><B>VAST+ display</B></A> groups 3D-similar structures based on their degree of similarity (complete or partial) to the <A HREF="#OutputBiologicalUnit"><B>biological unit</B></A> of the query structure; <A HREF="#OutputSortOptions"><B>ranks</B></A> them by the number of protein molecules in the query that simultaneously match the 3D shape of protein molecules in the VAST neighbor (<A HREF="#IllustratedExamples"><span style="color:#d70000">illustrated examples</span> of VAST+ results</A>); and enables you to view the sequence alignments and 3D superpositions of the biological units. Read more about the <A HREF="#Compare"><B>difference between VAST and VAST+</B></A>.)</I></BLOCKQUOTE -->
|
||
|
||
An <B>example</B> of the <B>original style VAST display</B> is <A HREF="#OriginalVASTIllustration"><span style="color:#d70000"><I>illustrated below</I></A>.<BR>
|
||
|
||
<UL>
|
||
|
||
<LI><B>Part 1</B> of the illustration shows <B>colored bars</B> that represent the <B>compact substructures</B>, or <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains"><B>3D domains</B></A>, detected by VAST in the query structure's protein molecule(s). These 3D domains serve as the fundamental unit of structure comparison. (The <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing">data processing</A>:<A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingGeometricalFeatures">geometrical features</A> section of the <A HREF="../../MMDB/docs/mmdb_help.html">MMDB help document</A> provides more information about how the 3D domains and similar structures are identified.) To view the 3D domains that have been identified in a protein molecule, open the MMDB <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">structure summary</A> page for a structure of interest, sroll down to the table of <A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents">molecules and interactions</A>, and click on the "<A HREF="../../MMDB/docs/mmdb_help.html#MmdbsrvProteinsShowAnnotation">show annotation</A>" link for the protein of interest. (For example, open the <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1PTH">structure summary page for 1PTH</A>.)</LI><BR>
|
||
|
||
<LI><B>Part 2</B> of the illustration shows the original-style VAST display, which consists of a <B>table summarizing the protein molecules and <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domain</A></B> in the query structure, and the number of structures that are geometrically similar to each individual protein molecule or 3D domain in your query structure. For any protein molecule or 3D domain of interest, click on the link in the "# of Related Structures" column to view a list of similar structures. The list includes a graphical display of alignment footprints and provides options to view sequence alignments and superposed structures.<!-- Original VAST does <B>not</B> group the results based on degree of similarity to the <A HREF="#OutputBiologicalUnit">biological unit</A> of the query structure. --></LI>
|
||
|
||
</UL>
|
||
|
||
To explore the example interactively, you can <A HREF="/Structure/vastplus/vastplus.cgi?uid=1PTH&style=old">open a live web page with original-style VAST results for 1PTH</A>, or
|
||
click on the image below to open an <A HREF="../../MMDB/docs/data/vast_alignment_of_1PTH_A_and_1EQG_A.cn3">interactive view of the 3D alignment of 1PTH's protein A, domain 1 and a sample similar structure, 1EQG</A> (Ovine Cox-1 Complexed With Ibuprofen). (Please note that <A HREF="../../CN3D/cn3d.shtml">Cn3D</A> 4.3.1 must be installed in your computer in order for the file to open. The <A HREF="../../CN3D/cn3dtut.shtml">Cn3D Tutorial</A> provides additional details about <A HREF="../../CN3D/cn3dtutP4.shtml">viewing structure alignments in Cn3D</A>.)<BR><BR>
|
||
<!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1PTH">1PTH</A -->
|
||
<!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1EQG">1EQG</A -->
|
||
|
||
The original style VAST display is still accessible by clicking the <B>"Original VAST" button</B> <!-- in the grey "Similar Structures" header bar at --> near the top of a VAST+ search results display<!-- or by the <A HREF="../../VAST/vasthelp.html#VASTHow">additional methods</A> described in the <A HREF="../../VAST/vasthelp.html">original VAST help document</A -->. The features, functions, and graphics of the original style VAST display are described in the <A HREF="../../VAST/vasthelp.html">original VAST help document</A>.<BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- ======== BOXED_NOTE_OUTPUT_ORIGINAL_VAST_ILLUSTRATED_EXAMPLE ======== -->
|
||
|
||
<A NAME="OriginalVASTDisplayIllustration"></A>
|
||
<A NAME="OriginalVASTIllustration"></A>
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
|
||
|
||
<TR>
|
||
<TD class="WhiteCell" ALIGN="Center" VALIGN="TOP">
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="5" class="WhiteCell NormalText3">
|
||
<TR>
|
||
<TD class="WhiteCell" WIDTH="10" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
<TD class="WhiteCellBlueEdgeAll" ALIGN="Left" VALIGN="TOP">
|
||
<P class="indent20bottomspace NormalText3"><B>Example</B> - Original style VAST display (as of 07 November 2013) for <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=50885"><B>1PTH</B></A>, "The Structural Basis of Aspirin Activity Inferred From the Crystal Structure of Inactivated Prostaglandin H2 Synthase" (sheep prostaglandin H2 synthase)<BR><BR>
|
||
|
||
|
||
<A HREF="../../MMDB/docs/data/vast_alignment_of_1PTH_A_and_1EQG_A.cn3"><IMG SRC="images/1PTH_structure_summary_vast_related_structures_individual_chains.png" WIDTH="800" HEIGHT="800" BORDER="0" 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, 1EQG (Ovine Cox-1 Complexed With Ibuprofen). Install Cn3D before clicking, if that program is not yet on your computer."></A><BR><BR>
|
||
|
||
<I><A HREF="/Structure/vastplus/vastplus.cgi?uid=1PTH&style=old">Open a live web page with original-style VAST results for 1PTH.</A></I><BR>
|
||
|
||
<!-- BR><A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=88951"><B>3O6F</B></A> Crystal Structure of a Human Autoimmune TCR Ms2-3c8 Bound to MHC Class II Self-ligand Mbphla-dr4:<BR><BR>
|
||
<IMG SRC="images/______" WIDTH="600" HEIGHT="200" BORDER="0" ALT="________"><BR>
|
||
<A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=88951&ShowOp=VastSum">open a live web page with original-style VAST results for 3O6F</A --></P>
|
||
</TD>
|
||
<TD class="WhiteCell" WIDTH="5" ALIGN="Center" VALIGN="TOP"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
<!-- === END_BOXED_NOTE_GRAPHICAL_DISPLAYS_ORIGINAL_VAST_ILLUSTRATED_EXAMPLE === -->
|
||
|
||
<TR>
|
||
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
||
|
||
<BLOCKQUOTE><I>In contrast to the original VAST display shown above, which focuses on similarities between individual protein molecules or 3D domains, the newer <A HREF="../vastplus/docs/vastplus_help.html#Output"><B>VAST+ display</B></A> groups 3D-similar structures based on their degree of similarity (complete or partial) to the <B>macromolecular complex</B> (<A HREF="../vastplus/docs/vastplus_help.html#OutputBiologicalUnit">biological unit</A>) of the query structure; <A HREF="../vastplus/docs/vastplus_help.html#OutputSortOptions">ranks</A> them by the number of protein molecules in the query that simultaneously match the 3D shape of protein molecules in the VAST neighbor; and enables you to view the <A HREF="../vastplus/docs/vastplus_help.html#SeqAlignView">sequence alignments</A> and <A HREF="../vastplus/docs/vastplus_help.html#3DView">3D superpositions</A> of the biological units. The <A HREF="../vastplus/docs/vastplus_help.html">VAST+ help document</A> provides <A HREF="../vastplus/docs/vastplus_help.html#IllustratedExamples"><span style="color:#d70000">illustrated examples</span> of VAST+ results</A> and additional details about the <A HREF="../vastplus/docs/vastplus_help.html#Compare">difference between VAST and VAST+</A>.</I></BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- === END_BOXED_NOTE_GRAPHICAL_DISPLAYS_ORIGINAL_VAST_ILLUSTRATED_EXAMPLE === -->
|
||
|
||
<!-- ========= END_LEVEL_1_LEVEL_1_ORIGINAL_STYLE_VAST_DISPLAY ========== -->
|
||
|
||
|
||
<!-- ====== 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 MiniText"> </TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ########### BLUE_HEADER_SECTION_6_ALGORITHM_DETAILS ############# -->
|
||
|
||
<A NAME="Algorithm"></A>
|
||
|
||
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1">VAST+ Algorithm</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_ALGORITHM_DETAILS ############ -->
|
||
|
||
|
||
<!-- ########## 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">
|
||
|
||
<!-- ============ MINI_TOC_FOR_THIS_SECTION ============== -->
|
||
<BR>
|
||
<BLOCKQUOTE>
|
||
|
||
<A HREF="#AlgorithmOverview">overview</A> | <A HREF="#AlgorithmIllustration"><I><span style="color:#d70000">illustration</span></I></A> | <A HREF="#AlgorithmDetails">additional details</A> | <A HREF="#AlgorithmAlignment">3D alignments</A> (<A HREF="#AlgorithmAlignmentInitial">initial alignment (all matching molecules superposed)</A>, <A HREF="#AlgorithmAlignmentRefined">refined alignment (invariant substructure superposed)</A>) | <A HREF="#AlgorithmSizeLimit">size limits</A> (<A HREF="#AlgorithmSizeLimitMinimum">minimum</A>, <A HREF="#AlgorithmSizeLimitMaximum">maximum</A>)
|
||
|
||
<!-- UL>
|
||
|
||
<LI><A HREF="#AlgorithmOverview">Overview of method used to identify similarly shaped macromolecular complexes of more than one protein</A></LI>
|
||
|
||
<LI><A HREF="#AlgorithmIllustration"><I><span style="color:#d70000">Illustration</span></I> of method used to identify similarly shaped macromolecular complexes</A></LI>
|
||
|
||
<LI><A HREF="#AlgorithmDetails">Additional details about the method used to identify similarly shaped macromolecular complexes of more than one protein</A></LI>
|
||
|
||
<UL>
|
||
<LI><A HREF="______">_____@@@@@_____</A> (<A HREF="______">__________</A>, <A HREF="______">__________</A>)</LI>
|
||
</UL>
|
||
|
||
</UL -->
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
||
|
||
<!-- ============== LEVEL_1_TOPIC_1_XXXXXX ================ -->
|
||
|
||
<A NAME="AlgorithmOverview"></A>
|
||
|
||
<BR>
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Overview of method used to identify similarly shaped macromolecular complexes</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>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
|
||
<A HREF="../vastplus.cgi"><B>VAST+</B></A> is a tool designed to compare 3-dimensional structures, with an emphasis on finding those with <B>similar macromolecular complexes</B> of more than one protein. The similarities are calculated using <B>purely geometric criteria</B>, without regard to sequence similarity, and therefore can identify distant homologs.<!--The similarities are calculated using purely geometric criteria, and therefore can identify distant homologs that cannot be recognized by sequence comparison. --><BR><BR>
|
||
|
||
VAST+ is built upon the original <A HREF="../../VAST/vast.shtml"><B>Vector Alignment Search Tool</B> (<B>VAST</B>)</A>. While original VAST finds 3D similarities between <B>individual protein molecules</B> or <B>individual</B> <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains"><B>3D domains</B></A>, VAST+ expands the capabilities of that program by making it possible to find macromolecular structures that have similarly shaped <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit"><B>biological units</B></A> (also referred to as "biounits"), using the method <I><A HREF="#AlgorithmIllustration"><span style="color:#d70000">illustrated</span></A></I> below. The section after the illustration provides <A HREF="#AlgorithmDetails">additional details</A> about the various steps in the process. The <B>similar structures</B> found by VAST and VAST+ are often referred to as "<B>neighbors</B>."<BR><BR>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
|
||
<!-- =============== END_LEVEL_1_TOPIC_1_XXXXXX =============== -->
|
||
|
||
<!-- ============== LEVEL_1_TOPIC_1_XXXXXX ================ -->
|
||
|
||
<A NAME="AlgorithmIllustration"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Illustration:  VAST+ algorithm<!-- builds upon original VAST results; method used to identify similarly shaped macromolecular complexes --></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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|
||
<BR>
|
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<TABLE width="750" style="margin:0px 0px 0px 0px;" class="NormalText">
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<TD width="50"> </TD>
|
||
<TD>
|
||
<IMG SRC="images/algorithm_schematic_vastplus_alignment_refinement.png" WIDTH="700" HEIGHT="2200" BORDER="1" ALT="Illustration of the VAST+ algorithm; overview of the method used to identify similarly shaped macromolecular complexes, and to generate initial and refined 3D alignments of superposed structures.">
|
||
</TD>
|
||
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|
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|
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|
||
<TD colspan="2" class="MiniText"> </TD>
|
||
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|
||
|
||
<TR>
|
||
<TD width="50"> </TD>
|
||
<TD>
|
||
<P class="indent50"><I>NOTE: You can use <A HREF="/Structure/icn3d/icn3d.html"><B>iCn3D</B></A> to open an <SPAN style="background-color: #FFFF00"><A HREF="/Structure/icn3d/full.html?align=1hho,4n7n&atype=0">interactive view of the <B>initial alignment</B> of 1HHO and 4N7N</A></SPAN>, and an <SPAN style="background-color: #FFFF00"><A HREF="/Structure/icn3d/full.html?align=1hho,4n7n&atype=1">interactive view of the <B>refined alignment</B> of 1HHO and 4N7N</A></SPAN><!-- A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1HHO"><B>1HHO</B></A> and <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=4N7N"><B>4N7N</B></A -->, which are the sample structures for human oxy- and deoxyhemoglobin that are featured in the illustration above.</I></P>
|
||
<!-- P class="indent50"><I>NOTE: If you have <A HREF="../../CN3D/cn3d.shtml"><B>Cn3D 4.3.1</B></A> installed on your computer, you can open an <A HREF="data/1HHO_and_4N7N_vastplus_ORIGINAL_alignment_cn3d_4_3_1.cn3"><B>interactive view of the initial alignment</B></A>, and an <A HREF="data/1HHO_and_4N7N_vastplus_REFINED_alignment_cn3d_4_3_1.cn3"><B>interactive view of the refined alignment</B></A>, of 1HHO and 4N7N, which are the sample structures for human oxy- and deoxyhemoglobin that are featured in the illustration above.</I></P -->
|
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||
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||
<A NAME="AlgorithmDetails"></A>
|
||
|
||
<P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Additional details about the method used to identify similarly shaped macromolecular complexes</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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<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
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<BLOCKQUOTE>
|
||
|
||
The process of identifying similar macromolecular complexes includes the following steps:
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="AlgorithmMMDBDataProcessing"></A><A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing">MMDB Data Processing</A>:<!-- img SRC="../../IMG/spacer.gif" width="50" 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>
|
||
|
||
<UL>
|
||
|
||
<LI>Identifies <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingGeometricalFeatures"><B>geometrical features</B></A> within a structure:</LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingSecondaryStructures"><B>secondary structures</B></A></LI>
|
||
|
||
<LI><A HREF="../../MMDB/docs/mmdb_help.html#DataProcessing3dDomains"><B>3D domains</B></A></LI>
|
||
|
||
</UL>
|
||
|
||
<LI>Identifies <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms"><B>biological units</B></A> within a structure</LI>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="AlgorithmVAST"></A><A NAME="AlgorithmOriginalVAST"></A><!-- A HREF="#OriginalVAST" --><A HREF="../../VAST/vast.shtml">Original VAST</A>:<!-- img SRC="../../IMG/spacer.gif" width="50" 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>
|
||
|
||
<UL>
|
||
|
||
<LI>Compares the shape of <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingSimilarStructures" --><A HREF="#OriginalVAST"><B>individual 3D domains</B> and <B>individual protein molecules</B></A> throughout the Molecular Modeling Database. <I>(Details about the original VAST algorithm are provided in the <A HREF="#References">references</A> noted at the end of this file and in the original <A HREF="../../VAST/vasthelp.html">VAST help document</A>.)</I></LI>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="AlgorithmVASTplus"></A><A HREF="../vastplus.cgi">VAST+</A>:<!-- img SRC="../../IMG/spacer.gif" width="50" 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>
|
||
|
||
<UL>
|
||
|
||
<LI>Compares the shape of <B>oligomers</B> throughout the Molecular Modeling Database, using the method <I><A HREF="#AlgorithmIllustration"><span style="color:#d70000">illustrated</span></A></I> above.</A></LI>
|
||
|
||
<UL>
|
||
|
||
<LI>Finds structures that have a <A HREF="#OutputFilterCompleteMatch"><B>complete match</B></A> to the query structure's biological unit</LI>
|
||
|
||
<LI>Finds structures that have a <A HREF="#OutputFilterPartialMatch"><B>partial match</B></A> to the query structure's biological unit</LI>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="AlgorithmScore"></A>Calculates <B>scores</B>, and use these to <A HREF="#OutputRankedList"><!-- A HREF="#OutputSortOptions" -->rank and sort hits</A> by:</LI>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="AlgorithmScoreAlignedProteins"></A><A HREF="#SortOptionAlignedProteins">number of <B>aligned proteins</B></A></LI>
|
||
|
||
<LI><A NAME="AlgorithmScoreRMSD"></A><A HREF="#SortOptionRMSD"><B>RMSD</B></A></LI>
|
||
|
||
<LI><A NAME="AlgorithmScoreAlignedResidues"></A><A HREF="#SortOptionAlignedResidues">number of <B>aligned residues</B></A></LI>
|
||
|
||
<LI><A NAME="AlgorithmScoreSequenceIdentity"></A><A HREF="#SortOptionSequenceIdentity">percent <B>sequence identity</B></A></LI>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="AlgorithmAlignment"></A><A NAME="3DAlignment"></A><A NAME="Superposition"></A>Generates a <!-- A HREF="#3DView" --><B>3D alignment</B> of biological units (macromolelcular complexes), as shown in the 4th and 5th sections of the <I><A HREF="#AlgorithmIllustration"><span style="color:#d70000">illustration</span></A></I> above</LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="AlgorithmAlignmentInitial"></A><A NAME="AlgorithmInitialAlignment"></A><A NAME="InitialAlignment"></A><A NAME="OriginalAlignment"></A><B>Initial alignment</B> (all matching molecules superposed): <img SRC="../../IMG/spacer.gif" width="50" 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><BR>
|
||
|
||
<UL>
|
||
<LI>The initial superposition of a query structure and its VAST+ neighbor uses the <B>complete set of individually aligned macromolecules</B> and corresponding matching amino acids to calculate a superposition of the complex structures<!-- uses the <B>complete sets of aligned and matching amino acids</B> as determined by original VAST -->.</LI><BR>
|
||
|
||
<LI>The spatial distance between the structures is then calculated as the <B>root-mean-square deviation (RMSD)</B>, which is a measure of the average distance between the atoms (equivalent C-alpha atoms) of the superposed proteins.</LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>For <B>example</B>, when comparing the structures of <B>human hemoglobin</B> in the <B>oxy and deoxy form</B> (1HHO and 4N7N, respectively), a total of <B>572 amino acids</B> are aligned, with an <B>RMSD of 1.02 Angstroms</B>, as shown in the 4th section of the <I><A HREF="#AlgorithmIllustration"><span style="color:#d70000">illustration</span></A></I> above.</LI><BR>
|
||
|
||
<LI>You can use <A HREF="/Structure/icn3d/icn3d.html"><B>iCn3D</B></A> to open an <I><A HREF="/Structure/icn3d/full.html?align=1hho,4n7n&atype=0"><B>interactive view of the initial alignment</B> of 1HHO and 4N7N</A></I>, which are the sample structures for human oxy- and deoxyhemoglobin that are featured in the illustration above.<BR><BR>
|
||
<I>Note: After opening the interactive view, notice that the iCn3D URL ends with an "<A HREF="../../icn3d/docs/icn3d_help.html#URLFormatOptionalParameterAtype">atype</A>" parameter, which enables you to specify the desired <B>alignment type</B>. A value of "<B>atype=0</B>" loads the initial alignment. The <A HREF="../../icn3d/docs/icn3d_help.html">iCn3D help document</A> includes additional details about the <A HREF="../../icn3d/docs/icn3d_help.html#URLFormat">URL format</A> that can be used to open structures directly in iCn3D, including a list of <A HREF="../../icn3d/docs/icn3d_help.html#URLFormatOptionalParameters">optional parameters</A>, such as "atype" and more.</I></LI><BR>
|
||
|
||
<!-- LI><I>(You can <A HREF="data/1HHO_and_4N7N_vastplus_ORIGINAL_alignment_cn3d_4_3_1.cn3">open an <B>interactive view of the initial alignment</B> of 1HHO and 4N7N</A>[, the sample structures for human oxy- and deoxyhemoglobin that are featured in the <I><A HREF="#AlgorithmIllustration"><span style="color:#d70000">illustration</span></A></I> above].)</I></LI><BR -->
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="AlgorithmAlignmentRefined"></A><A NAME="AlgorithmRefinedAlignment"></A><A NAME="RefinedAlignment"></A><B>Refined alignment</B> (invariant substructure superposed): <img SRC="../../IMG/spacer.gif" width="50" 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><BR>
|
||
|
||
|
||
<UL>
|
||
<LI>Using the RMSD from the initial alignment as a <B>threshold</B>, VAST+ identifies a <B>subset set of amino acids</B> that have <B>highly similar 3D positions</B> in the query and subject <I>complex structure</I>, and uses it to create a refined alignment that allows identification and visualization of the most similar portion of the structures (the structurally invariant core of the assembly), as well as the differences between the structures.</LI><BR>
|
||
|
||
<LI>To do this, it finds <B>all amino acids pairs that have a distance equal to, or less than, the original RMSD</B>, and then regenerates the superposition to create a more finely tuned alignment for that subset of amino acids.</LI><BR>
|
||
|
||
<LI>As a result, the <B>total number of aligned amino acids</B> and the <B>RMSD</B> <B>generally decrease</B> compared to the initial alignment.</LI><BR>
|
||
|
||
<UL>
|
||
|
||
<LI>For <B>example</B>, the refined alignment of <B>human hemoglobin</B> in the <B>oxy and deoxy form</B> (<B>1HHO</B> and <B>4N7N</B>, respectively), has a total of <B>221 amino acids</B> aligned (compared to the initial 572), and an <B>RMSD of 0.39 Angstroms</B> (compared to the initial 1.02 Angstroms), as shown in the 5th (last) section of the <I><A HREF="#AlgorithmIllustration"><span style="color:#d70000">illustration</span></A></I> above.</LI><BR>
|
||
|
||
<LI>The <B>interpretation of the refined alignment</B> is that the alpha-beta dimers are the most stable part of the tetramer, in the oxy- vs. deoxy- tetramers. That is, the main conformational change is a shift in the relative positions of the alpha-beta dimers upon oxygen binding (or unbinding).</LI><BR>
|
||
|
||
<LI>This can be <B>readily visualized</B> in <A HREF="/Structure/icn3d/icn3d.html"><B>iCn3D</B></A> by opening an <I><A HREF="/Structure/icn3d/full.html?align=1hho,4n7n&atype=1"><B>interactive view of the refined alignment</B> of 1HHO and 4N7N</A></I> and then <B>toggling between the two structures</B> by clicking the <B>"Alternate Selection" button</B>.<BR><BR>
|
||
<I>Note: After opening the interactive view, notice that the iCn3D URL ends with an "<A HREF="../../icn3d/docs/icn3d_help.html#URLFormatOptionalParameterAtype">atype</A>" parameter, which enables you to specify the desired <B>alignment type</B>. A value of "<B>atype=1</B>" loads the refined alignment. The <A HREF="../../icn3d/docs/icn3d_help.html">iCn3D help document</A> includes additional details about the <A HREF="../../icn3d/docs/icn3d_help.html#URLFormat">URL format</A> that can be used to open structures directly in iCn3D, including a list of <A HREF="../../icn3d/docs/icn3d_help.html#URLFormatOptionalParameters">optional parameters</A>, such as "atype" and more.</I></LI><BR>
|
||
|
||
<!-- LI><I>(You can open an <A HREF="/Structure/icn3d/full.html?align=1hho,4n7n&atype=1"><B>interactive view of the <B>refined alignment</B></A> of 1HHO and 4N7N, which are the sample structures for human oxy- and deoxyhemoglobin that are featured in the illustration above.)</I></LI><BR -->
|
||
|
||
<!-- LI><I>(If you have <A HREF="../../CN3D/cn3d.shtml">Cn3D 4.3.1</A> installed on your computer, you can <A HREF="data/1HHO_and_4N7N_vastplus_REFINED_alignment_cn3d_4_3_1.cn3">open a <B>interactive view of the refined alignment</B> of 1HHO and 4N7N</A>[, the sample structures for human oxy- and deoxyhemoglobin that are featured in the <I><A HREF="#AlgorithmIllustration"><span style="color:#d70000">illustration</span></A></I> above].)</I></LI><BR -->
|
||
|
||
</UL>
|
||
|
||
<LI>In general, <B>there is not going to be a unique subset of amino acids</B> that have the best alignment. For example, in the hemoglobin tetramer case above, one subset (solution to the problem) is going to be (roughly) one of the alpha-beta dimers, another possibility is the other alpha-beta dimer.</LI><BR>
|
||
|
||
<LI>In either case, the refined alignment allows identification and visualization of the <B>most similar portion of the structures</B> (the <B>structurally invariant core</B> of the assembly), as well as the <B>differences between the structures</B>.</LI>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="AlgorithmSizeLimit"></A><A NAME="AlgorithmSizeLimits"></A><A NAME="SizeLimit"></A><A NAME="SizeLimits"></A><B>Size limits</B><!-- img SRC="../../IMG/spacer.gif" width="50" 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><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="AlgorithmSizeLimitMinimum"></A><B>Minimum</B> size of structures that are neighbored:</LI>
|
||
|
||
<UL>
|
||
<LI>VAST, and therefore VASTS+, only operates on protein molecules that contain three or more <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingSecondaryStructures">secondary structure</A> elements (SSEs)</LI>
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="AlgorithmSizeLimitMaximum"></A><B>Maximum</B> size of structures that are neighbored:</LI>
|
||
|
||
<UL>
|
||
<LI>VAST+ does not work on MMDB <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingMergeSplitFiles">merged structures</A>, because the <A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms">biological unit</A> of the complete structure is not specified in a computer readable way in the source PDB files. <I>(However, structures that are similar to the individual protein molecules within the merged structure have been calculated by original VAST. To access them, open the <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">MMDB structure summary page</A> for the merged structure of interest and click on the "Similar Structures: VAST+" button near the top of the page. The resulting page will display a note that "<A HREF="#NullResult">no VAST+ neighbors are available</A>," along with a table showing <A HREF="#OriginalVAST">Original VAST results</A>.)</I></LI>
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE>
|
||
<BR>
|
||
|
||
<!-- =============== END_LEVEL_1_TOPIC_1_XXXXXX =============== -->
|
||
|
||
<!-- ============== LEVEL_1_TOPIC_1_XXXXXX ================ -->
|
||
|
||
<A NAME="AlgorithmBiologicalUnits"></A>
|
||
|
||
<!-- P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Identify biological units within a 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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></A><B>_____________</B></LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE -->
|
||
|
||
<!-- =============== END_LEVEL_1_TOPIC_1_XXXXXX =============== -->
|
||
|
||
<!-- ============== LEVEL_1_TOPIC_1_XXXXXX ================ -->
|
||
|
||
<A NAME="AlgorithmCompleteSimilarity"></A>
|
||
|
||
<!-- P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Find structures that have a complete match to the query structure's biological unit </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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></A><B>_____________</B></LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE -->
|
||
|
||
<!-- =============== END_LEVEL_1_TOPIC_1_XXXXXX =============== -->
|
||
|
||
<!-- ============== LEVEL_1_TOPIC_1_XXXXXX ================ -->
|
||
|
||
<A NAME="AlgorithmPartialSimilarity"></A>
|
||
|
||
<!-- P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Find structures that have a partial match to the query structure's biological unit</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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></A><B>_____________</B></LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE -->
|
||
|
||
<!-- =============== END_LEVEL_1_TOPIC_1_XXXXXX =============== -->
|
||
|
||
<!-- ============== LEVEL_1_TOPIC_1_XXXXXX ================ -->
|
||
|
||
<A NAME="AlgorithmScore"></A>
|
||
<A NAME="AlgorithmScores"></A>
|
||
|
||
<!-- P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Calculate scores for matches</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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></A><B>_____________</B></LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE -->
|
||
|
||
<!-- =============== END_LEVEL_1_TOPIC_1_XXXXXX =============== -->
|
||
|
||
<!-- ============== LEVEL_1_TOPIC_1_XXXXXX ================ -->
|
||
|
||
<A NAME="AlgorithmSizeLimit"></A>
|
||
|
||
<!-- P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Size limits</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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="AlgorithmSizeLimitMinimum"></A><B>Minimum size</B> of structures that are neighbored</LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="AlgorithmSizeLimitMaximum"></A><B>Maximum size</B> of structures that are neighbored</LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE -->
|
||
|
||
<!-- =============== END_LEVEL_1_TOPIC_1_XXXXXX =============== -->
|
||
|
||
<!-- ============== LEVEL_1_TOPIC_1_XXXXXX ================ -->
|
||
|
||
<A NAME="AlgorithmSuperpositionBiounit"></A>
|
||
|
||
<!-- P class="indent20">
|
||
<SPAN class="HeaderText3"><B>Determine optimal superposition of biological units (macromolecular complexes)</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>
|
||
<BR>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
||
<TR>
|
||
<TD>
|
||
|
||
<BLOCKQUOTE>
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.<BR><BR>
|
||
|
||
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 text text text.
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="AlgorithmSizeLimitMinimum"></A><B>Minimum size</B> of structures that are neighbored</LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
<LI><A NAME="AlgorithmSizeLimitMaximum"></A><B>Maximum size</B> of structures that are neighbored</LI><BR><BR>
|
||
|
||
<UL>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR><BR>
|
||
|
||
<LI><A NAME="_____________"></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 text text text</LI><BR>
|
||
|
||
</UL>
|
||
<BR>
|
||
|
||
</UL>
|
||
|
||
</BLOCKQUOTE>
|
||
|
||
</TD>
|
||
</TR>
|
||
</TABLE -->
|
||
|
||
<!-- =============== END_LEVEL_1_TOPIC_1_XXXXXX =============== -->
|
||
|
||
<!-- ====== 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 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 MiniText"> </TD>
|
||
</TR>
|
||
</TABLE -->
|
||
|
||
<!-- ================== END_VERTICAL SPACER ===================== -->
|
||
|
||
<!-- ########### BLUE_HEADER_SECTION_7_DEFINITIONS_GLOSSARY ############# -->
|
||
|
||
<A NAME="Definition"></A>
|
||
<A NAME="Definitions"></A>
|
||
<A NAME="Glossary"></A>
|
||
|
||
<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
||
<TR>
|
||
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Glossary</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_DEFINITIONS ############ -->
|
||
|
||
|
||
<!-- ########## 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" -->
|
||
|
||
<!-- see list of terms in
|
||
/Structure/VAST/vasthelp.html#VASTTable -->
|
||
|
||
<!-- ============ MINI_TOC_ALPHABETICAL_LIST_OF_TERMS_IN_GLOSSARY ============== -->
|
||
|
||
<!-- BLOCKQUOTE>
|
||
|
||
<BR>
|
||
|
||
<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="#Definition%Id">%Id</A><BR>
|
||
<A HREF="#Definition3DDomain">3D Domain</A><BR>
|
||
<A HREF="#DefinitionAlignedLength">[<A HREF="#DefinitionAlignmentLength">]Aligned Length</A><BR>
|
||
<A HREF="#DefinitionBiologicalUnit">Biological Unit</A><BR>
|
||
<A HREF="#DefinitionDescription">Description</A><BR>
|
||
</TD>
|
||
|
||
<TD WIDTH="33%" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="#DefinitionGSP">GSP</A><BR>
|
||
<A HREF="#DefinitionLHM">LHM</A><BR>
|
||
<A HREF="#DefinitionPVal">P-VAL</A><BR>
|
||
<A HREF="#DefinitionQuaternaryStructure">Quaternary Structure</A><BR>
|
||
<A HREF="#DefinitionRelatedStructures">Related Structures</A><BR>
|
||
<A HREF="#DefinitionRMSD">RMSD</A><BR>
|
||
</TD>
|
||
|
||
<TD WIDTH="33%" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
|
||
<A HREF="#DefinitionScore">Score</A><BR>
|
||
<A HREF="#DefinitionSimilarStructures">Similar Structures</A><BR>
|
||
<A HREF="#DefinitionVAST">VAST</A><BR>
|
||
<A HREF="#Definition______">__________</A><BR>
|
||
<A HREF="#Definition______">__________</A><BR>
|
||
<A HREF="#Definition______">__________</A><BR>
|
||
</TD>
|
||
|
||
</TR>
|
||
|
||
</TABLE>
|
||
|
||
</BLOCKQUOTE -->
|
||
|
||
<!-- ========== END_MINI_TOC_ALPHABETICAL_LIST_OF_TERMS_IN_GLOSSARY ============ -->
|
||
|
||
<!-- ============== LEVEL_1_GLOSSARY_DEFINITIONS ================ -->
|
||
|
||
<A NAME="______________"></A>
|
||
|
||
<!-- P class="indent20">
|
||
<SPAN class="HeaderText3"><B>______________</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>
|
||
<BR -->
|
||
|
||
<!-- ========== 2_COLUMN_TABLE =============== -->
|
||
|
||
<!-- BLOCKQUOTE>
|
||
|
||
<TABLE style="margin:0px 0px 0px 0px;" class="TableText1" border="0" cellpadding="0" cellspacing="20">
|
||
[<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>Term</b></TD>
|
||
<TD class="format1H" align="center" style="white-space: nowrap;"><b>Definition</b></TD>
|
||
</TR>]
|
||
|
||
<!-- ============= DEFINITION_%Id ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="Definition%Id"></A><B>%Id</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_3DDomain ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="Definition3DDomain"></A><B>3D Domain</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_AlignedLength ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionAlignedLength"></A><A NAME="DefinitionAlignmentLength"></A><B>Aligned Length</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_BiologicalUnit ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionBiologicalUnit"></A><B>Biological Unit</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_Description ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionDescription"></A><B>Description</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_GSP ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionGSP"></A><B>GSP</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_LHM ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionLHM"></A><B>LHM</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_P-Val ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionPVal"></A><B>P-Val</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_QuaternaryStructure ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionQuaternaryStructure"></A>[<B>Quaternary Structure</B>]</TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_RelatedStructures ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionRelatedStructures"></A><B>Related Structures</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_RMSD ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionRMSD"></A><B>RMSD</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_Score ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionScore"></A><B>Score</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_SimilarStructures ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionSimilarStructures"></A><B>Similar Structures</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_VAST ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="DefinitionVAST"></A><B>VAST</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= DEFINITION_XXXXXX ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="Definition______"></A><B>______Column1__________</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= XXXXXX_NO_UP_ARROW ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="Definition______"></A><B>______Column1__________</B></TD>
|
||
<TD valign="top">______Column2__________</TD>
|
||
</TR -->
|
||
|
||
<!-- ============= XXXXXX_WITH_UP_ARROW ============== -->
|
||
|
||
<!-- TR>
|
||
<TD valign="top" style="white-space: nowrap;" rowspan="1"><A NAME="Definition______"></A><B>______Column1__________</B></TD>
|
||
<TD valign="top">
|
||
<A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></IMG></A>
|
||
______Column2__________<BR><BR>
|
||
</TD>
|
||
</TR -->
|
||
|
||
<!-- ========= XXXXXX_WITH_IMAGE_PLACEHOLDER_IN_COLUMN1 ========= -->
|
||
|
||
<!-- TR>
|
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<td width="110" class="NormalText" align="left" valign="top">27 July 2016</td>
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<td class="NormalText" align="left" valign="top">A new version of <A HREF="../vastplus.cgi"><B>VAST+</B></A> was released. It provides a <A HREF="#AlgorithmAlignmentRefined">refined structure-based alignment</A> of similar macromolecular complexes, and displays the 3D superpositions in the recently released <A HREF="../../icn3d/docs/icn3d_about.html">iCn3D</A>, a WebGL-based structure viewer. The <A HREF="#AlgorithmAlignmentInitial">initial alignment</A> of similar macromolecular complexes, which became available with the first release of VAST+, uses the complete set of <I>individually aligned macromolecules</I> and corresponding matching amino acids to calculate a superposition of the complex structures. In contrast, the new release of VAST+ identifies a <I>subset set of amino acids</I> that have <I>highly similar 3D positions</I> in the query and subject <I>complex structure</I>, and uses it to create a <A HREF="#AlgorithmAlignmentRefined">refined alignment</A> that allows identification and visualization of the most similar portion of the structures (the <B>structurally invariant core</B> of the assembly), as well as the differences between the structures.<BR><BR>
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An <A HREF="#AlgorithmIllustration"><I><!-- span style="color:#d70000" -->illustration<!-- /span --></I></A> summarizes the general concepts in the VAST+ algorithm and includes an example of the initial alignment, as well as the refined alignment, for 1HHO and 4N7N (oxy- and deoxy- forms of human hemoglobin).<BR><BR>
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iCn3D provides an <A HREF="/Structure/icn3d/full.html?align=1hho,4n7n&atype=0"><I>interactive view of the initial alignment</I></A>, and an <A HREF="/Structure/icn3d/full.html?align=1hho,4n7n&atype=1"><I>interactive view of the refined alignment</I></A>, of 1HHO and 4N7N, which are the sample structures for human oxy- and deoxyhemoglobin featured in the illustration mentioned above.
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<!-- I>Note: If you have <A HREF="../../CN3D/cn3d.shtml">Cn3D 4.3.1</A> installed on your computer, you can open a <A HREF="data/1HHO_and_4N7N_vastplus_ORIGINAL_alignment_cn3d_4_3_1.cn3">interactive view of the initial alignment</A>, and a <A HREF="data/1HHO_and_4N7N_vastplus_REFINED_alignment_cn3d_4_3_1.cn3">interactive view of the refined alignment</A>, of 1HHO and 4N7N.</I --></td>
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<td width="110" class="NormalText" align="left" valign="top">01 NOV 2013</td>
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<td class="NormalText" align="left" valign="top">Initial release of <A HREF="../vastplus.cgi"><B>VAST+</B></A>, a tool that identifies macromolecules that have similar 3-dimensional structures, with an emphasis on finding similar macromolecular complexes. The similarities are calculated using purely geometric criteria, without regard to sequence similarity, and therefore can identify distant homologs. VAST+ is built upon the original <A HREF="../../VAST/vast.shtml">Vector Alignment Search Tool (VAST)</A>, and expands the capabilities of that program by taking into account the <!-- A HREF="../../MMDB/docs/mmdb_help.html#DataProcessingBiologicalForms" --><A HREF="#OutputBiologicalUnit">biological unit</A> ("biounit") of each structure, not just individual protein molecules or their substructures. A recent <A HREF="/pubmed/24319143">publication</A> provides details and this VAST+ help document includes a <A HREF="#Compare">comparison</A> of original VAST and VAST+, as well as <A HREF="#DatabaseApplications">examples of how can VAST+ be used to learn more about proteins</A>. <I>(Please note: in order to view the 3D superpositions of similar biological units, you must install the most recent version of the NCBI molecular viewing software, <A HREF="../../CN3D/cn3d.shtml">Cn3D 4.3.1</A>.)<BR><BR>
|
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The <A HREF="../../VAST/vastsearch.html"><!-- A HREF="../../VAST/vastsrchelp.html" --><B>VAST Search</B></A> tool, which accepts input of a query structure's 3D coordinates and returns original-style VAST results, continues to be available.
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<A NAME="References"></A>
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
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<TD class="SteelBlueCell"><SPAN class="HeaderText1">References</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>
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<!-- ================= LEVEL_1_REFERENCES_CITING ==================== -->
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<A NAME="Citing"></A>
|
||
<BR><BR>
|
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<P class="indent20">
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<SPAN class="HeaderText3"><B>Citing VAST:</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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<BR>
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<!-- =========== LEVEL_2_TABLE_OF_REFERENCES_CITING ============== -->
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<A NAME="CitingVAST"></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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<!-- =========== CITING_VAST+ ============= -->
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<TD colspan="2" align="left" class="HeaderText2A">Citing VAST+</TD>
|
||
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|
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|
||
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|
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<TD width="18" valign="top" align="left"><A NAME="VASTplus_2014_NAR"></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>
|
||
<TD valign="top" align="left"><!-- SPAN class="ThumbText2">Citing VAST+</SPAN>:   --><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></B> (Epub 2013 Dec 6) doi: 10.1093/nar/gkt1208 <!-- <B>2014</B> Jan; V(I): PPP-PP. --> [PubMed PMID: 24319143]</A> <A HREF="http://nar.oxfordjournals.org/content/early/2013/12/05/nar.gkt1208.full">[Full Text]</A></TD>
|
||
</TR>
|
||
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||
<TR>
|
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<TD colspan="2" align="left" class="MicroText"> </TD>
|
||
</TR>
|
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<!-- =========== CITING_ORIGINAL_VAST_RESOURCE ============= -->
|
||
|
||
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<TD colspan="2" align="left" class="HeaderText2A">Citing Original VAST</TD>
|
||
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|
||
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||
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||
<TD width="18" valign="top" align="left"><A NAME="VAST_Surprising_Similarities_1996"></A><A HREF="/pubmed/8804824?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"><!-- SPAN class="ThumbText2">Citing Original VAST</SPAN>:   --><A HREF="/pubmed/8804824?dopt=AbstractPlus">Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. <B><I>Curr Opin Struct Biol.</I> 1996</B> Jun; 6(3): 377-85. [PubMed PMID: 8804824]</A> <!-- A HREF="__________">[Full Text]</A --></TD>
|
||
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|
||
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<TD colspan="2" align="left" class="MicroText"> </TD>
|
||
</TR>
|
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|
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<!-- =========== CITING_VAST_SIMILARITY_SCORES ============= -->
|
||
|
||
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<TD colspan="2" align="left" class="HeaderText2A">Citing similarity scores</TD>
|
||
</TR>
|
||
|
||
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|
||
<TD width="18" valign="top" align="left"><A NAME="CitingVASTSimilarityScores_2004"></A><A HREF="/pubmed/15382231?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"><!-- SPAN class="ThumbText2">Citing similarity scores</SPAN>:   --><A HREF="/pubmed/15382231?dopt=AbstractPlus">Panchenko AR, Madej T. Analysis of protein homology by assessing the (dis)similarity in protein loop regions. <B><I>Proteins</I> 2004</B> Nov 15; 57(3): 539-47. [PubMed PMID: 15382231]</A> <A HREF="/pmc/articles/PMC1994810/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD colspan="2" align="left" class="MicroText"> </TD>
|
||
</TR>
|
||
|
||
<!-- ======= CITING_VAST_HOMOLOGOUS_LOOPS_AND_CORES ========= -->
|
||
|
||
<TR>
|
||
<TD colspan="2" align="left" class="HeaderText2A">Citing homologous cores and loops</TD>
|
||
</TR>
|
||
|
||
<TR>
|
||
<TD width="18" valign="top" align="left"><A NAME="CitingVASTHomologousCoresAndLoops_2007"></A><A HREF="/pubmed/17425794?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"><!-- SPAN class="ThumbText2">Citing homologous cores and loops</SPAN>:   --><A HREF="/pubmed/17425794?dopt=AbstractPlus">Madej T, Panchenko AR, Chen J, Bryant SH. Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins. <B><I>BMC Struct Biol.</I> 2007</B> Apr 10; 7(1): 23. [PubMed PMID: 17425794]</A> <A HREF="http://www.biomedcentral.com/1472-6807/7/23">[Full Text]</A>    <SPAN class="ThumbText"><I><A HREF="../../VAST/docs/vast_publications.html">more articles on VAST...</A></I></SPAN></TD>
|
||
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|
||
|
||
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|
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|
||
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|
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||
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||
</BLOCKQUOTE>
|
||
|
||
<!-- =============== LEVEL_1_REFERENCES_ADDITIONAL ================== -->
|
||
|
||
<A NAME="ReferencesAdditional"></A>
|
||
<A NAME="AdditionalReferences"></A>
|
||
|
||
<BR>
|
||
<P class="indent20">
|
||
<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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|
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<A NAME="____"></A>
|
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|
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<BLOCKQUOTE>
|
||
|
||
A separate page lists <A HREF="../../MMDB/docs/macromol_publications.html"><SPAN class="ThumbText2"><B>all publications</B></SPAN></A> about NCBI's <A HREF="../../MMDB/mmdb.shtml"><SPAN class="ThumbText2"><B>3D Macromolecular Structures Resources</B></SPAN></A>, including those listed here<!--, which are specific to the <A HREF="/structure"><SPAN class="ThumbText2"><B>Molecular Modeling Database</B></SPAN></A>, --> plus articles by the NCBI Structure group describing the results of <A HREF="../../structure_research.html"><SPAN class="ThumbText2"><B>computational biology research</B></SPAN></A> on the Molecular Modeling Database.<BR><BR><BR>
|
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<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></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"><B>___DATABASENAME___ --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
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<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></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"><B>___DATABASENAME___ --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
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<TD width="18" valign="top" align="left"><A NAME="DBNAME_NCBIHandbook"></A><A HREF="_____URL_to_the_book_chapter_____"><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="_____URL_to_the_book_chapter_____">Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. Chapter N IN The <I><B>NCBI Handbook</B></I> [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, <B>YYYY</B> Mmm. DD [revised YYYY Mmm. DD]. [cited YYYY Mmm DD]. Available from _____URL_to_the_book_chapter_____ in Entrez Books (/books)</A>.</TD>
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 17 November 2017</SPAN></TD>
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