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<meta name="description" content="Search methods for the Molecular Modeling Database (MMDB), a resource of the National Center for Biotechnology Information (NCBI) Structure Group" />
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<meta name="keywords" content="Molecular Modeling Database, MMDB, 3D Domains, Vector Alignment Search Tool, VAST, nrPDB, Cn3D structure viewing software, CBLAST, Entrez Protein related structure links, three-dimensional structures, 3D, 3-D, macromolecular structures, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, proteins, protein function, homologous, homologs, orthologs, nucleic acids, DNA, RNA, ligands, bound chemicals, drugs, medicine, Conserved Domain Database (CDD), CDTree, CD Tree, NCBI, National Center for Biotechnology Information" />
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<TD class="DocTitleText" align="left"> 3D Macromolecular Structures</TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../mmdb.shtml"> OVERVIEW </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="mmdb_how_to.html"> HOW TO </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="//ftp.ncbi.nih.gov/mmdb"> FTP </A></TD>
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<TD class="WhiteCell" ALIGN="LEFT" VALIGN="TOP">
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<SPAN class="NormalText2"> <BR></SPAN>
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<P class="indent20 TOCText2">There are several ways to <B>search</B> the Molecular Modeling Database (MMDB):</P></TD>
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</TR>
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<!-- ########## END_WHITE_HEADER ########## -->
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<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
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<!-- TR>
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<TD class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
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<P class="indent10 NormalText">Description of <A HREF="___">resource</A> text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text.</P>
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</TD>
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</TR -->
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<TD class="WhiteCell MiniText" ALIGN="Center" VALIGN="TOP"> </TD>
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<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
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<TR>
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<TD width="10" class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
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 </TD>
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<TD width="180" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="QueryTextTerm"></A>
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<A HREF="/structure">text term search</A></TD>
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<TD class="WhiteCell NormalText3" ALIGN="LEFT" VALIGN="TOP">
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Use the query box above or the <A HREF="/structure"><B>Entrez Structure</B></A> page to search the Molecular Modeling Database (<!-- A HREF="/structure" -->MMDB) by key word (e.g., tumor suppressor), accession number, author name, journal name, and more. The <A HREF="mmdb_help.html"><B>MMDB help document</B></A> provides <A HREF="mmdb_help.html#SearchTips">search tips</A>.<!-- The <A HREF="mmdb_help.html"><B>MMDB help document</B></A> provides details about types of queries (basic, advanced, complex Boolean), search fields, and more. --></TD>
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<TD width="5" class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
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 </TD>
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</TR>
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<TR>
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<TD colspan="4" class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TR>
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<TD width="10" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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 </TD>
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<TD width="180" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="QueryProteinSequence"></A>
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<A HREF="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&DATABASE=pdb">protein sequence query</A></TD>
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<TD class="WhiteCell NormalText3" ALIGN="LEFT" VALIGN="TOP">
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Use <A HREF="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&DATABASE=pdb"><B>protein BLAST</B></A> to compare a query protein sequence against the protein sequences extracted from <A HREF="http://www.rcsb.org/pdb/"><B>PDB</B></A> 3-dimensional structure records.<!-- (<A HREF="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs">BLAST help</A>) --> If your query protein sequence already exists in the <A HREF="/protein"><B>Entrez Protein</B></A> database, precalculated BLAST results are instantly available by opening the <B>Links</B> menu for your protein sequence of interest and selecting <B>Related Structures</B> (see frame B of <A HREF=" mmdb_how_to_search_by_gene.html "><span style="color:#d70000">illustrated example</span></A>). This will retrieve protein structures that are sequence-similar to your query.</TD>
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</TR>
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<TR>
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<TD colspan="4" class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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<TR>
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<TD width="10" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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 </TD>
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<TD width="180" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="Query3DCoordinates"></A>
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<A HREF="/Structure/VAST/vastsearch.html">3D coordinates for a newly resolved structure</A></TD>
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<TD class="WhiteCell NormalText3" ALIGN="LEFT" VALIGN="TOP">
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Use the <A HREF="../../VAST/vastsearch.html"><B>VAST Search</B></A> program to upload the 3D coordinates of a newly resolved structure in <!-- A HREF="http://www.rcsb.org/pdb/" --><A HREF="http://www.wwpdb.org/docs.html"><B>PDB format</B></A> and compare it against the 3D coordinates of structures already available in MMDB. This will retrieve similar 3D structures as determined by purely geometric criteria, regardless of the level of sequence similarity. You can then use the free <A HREF="/Structure/CN3D/cn3d.shtml"><B>Cn3D</B></A> program to view the similar structures superposed on your query.<BR><BR>
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If your structure is already publicly available in the <A HREF="/structure"><B>Entrez Structure</B> (MMDB)</A> database, then you can simply enter the structure's <A HREF="mmdb_help.html#MmdbsrvPDBID">PDB ID</A> or <A HREF="mmdb_help.html#MmdbsrvMMDBID">MMDB ID</A> on the <A HREF="../../VAST/vast.shtml"><B>VAST home page</B></A>, in order to retrieve other structures that contain similarly shaped individual protein molecules or <A HREF="mmdb_help.html#DataProcessing3dDomains">3D domains</A>, or on the <A HREF="../../vastplus/vastplus.cgi"><B>VAST+ home page</B></A>, in order to retrieve other structures that have similarly shaped <A HREF="../../vastplus/docs/vastplus_help.html#OutputBiologicalUnit">biological assemblies</A>. <!-- I>   Note that precalculated VAST Search results are also available for each protein structure in the <A HREF="/structure"><B>Entrez Structure</B> (MMDB)</A> database, allowing instant access to similar 3-dimensional structures. Simply follow the "<B>Related Structures</B>" link for any individual record in the document summary ("doscum") display of Entrez search results (e.g., <a HREF="/structure?cmd=search&term=p53%20tumor%20suppressor">P53 tumor suppressor</a>), or click on the <B>colored "Sequence..." bar</B> for any protein chain of interest on an MMDB structure summary page (e.g., <a HREF="/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=51571">1TUP</a>).</I --></TD>
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</TR>
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<TR>
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<TD colspan="4" class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TR>
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<TD width="10" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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 </TD>
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<TD width="180" class="WhiteCell TOCText2" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="FetchViaUID"></A>
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direct fetch via UID</TD>
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<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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Retrieve a 3D structure record directly from the backend database by entering its unique identifier (UID), in the form of a <A HREF="mmdb_help.html#MmdbsrvPDBID"><B>PDB ID</B></A> or <A HREF="mmdb_help.html#MmdbsrvMMDBID"><B>MMDB ID</B></A>, in the text box below:<BR>
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<TABLE style="margin:0px 0px 0px 0px;" border="0" cellspacing="1" cellpadding="0" class="WhiteCell ThumbText">
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<FORM METHOD="POST" ACTION="/Structure/mmdb/mmdbsrv.cgi">
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<TD CLASS="ThumbText" ALIGN="CENTER"><INPUT TYPE="TEXT" NAME="uid" SIZE="10"></TD>
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<TD CLASS="ThumbText" ALIGN="CENTER"><INPUT TYPE="SUBMIT" VALUE="Go"></TD>
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</TR>
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</FORM>
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<I>Note</I>: the "text term search" function also allows you to enter either of those unique identifiers (UIDs), but it first searches the Entrez indices for the UID, then retrieves the record. In contrast, the "direct fetch via UID" option bypasses the Entrez indices and simply retrieves the specified record.</TD>
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<TD colspan="4" class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD colspan="4" class="WhiteCell MiniText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD width="10" class="WhiteCell ThumbText2" ALIGN="LEFT" VALIGN="TOP">
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 </TD>
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<TD colspan="2" class="WhiteCell ThumbText2" ALIGN="LEFT" VALIGN="TOP">
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The "<a href="mmdb_how_to.html"><B>How To</B></a>" page provides <a href="mmdb_how_to.html"><B>quick start guides</B></a> for some common types of searches, and the <A HREF="mmdb_help.html"><B>MMDB Help document</B></a> provides additional <A HREF="mmdb_help.html#SearchTips">search tips</A>.<!-- detailed descriptions of the database content and search system, and display formats. --> 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>.</TD>
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<TD width="5" class="WhiteCell ThumbText2" ALIGN="LEFT" VALIGN="TOP">
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<!-- ====== Alternative, boxed format for footnote above ====== -->
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<TD colspan="2" class="WhiteCell ThumbText2" ALIGN="LEFT" VALIGN="TOP">
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell ThumbText">
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<TD class="WhiteCell" WIDTH="50" ALIGN="Center" VALIGN="TOP"> </TD>
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<TD class="WhiteCellBlueEdgeAll" ALIGN="CENTER" VALIGN="TOP">
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<SPAN class="MiniText"> <BR></SPAN>
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<P class="indent20bottomspace ThumbText2">The "<a href="mmdb_how_to.html"><B>How To</B></a>" page provides <a href="mmdb_how_to.html"><B>quick start guides</B></a> for some common types of searches, and the <a href="mmdb_help.html"><B>MMDB Help document</B></a> provides detailed descriptions of the database content, search system, and display formats. 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>
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<TD class="WhiteCell" WIDTH="50" ALIGN="Center" VALIGN="TOP"> </TD>
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<SPAN class="MiniText"> <BR></SPAN>
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Additional References</TD>
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</TR -->
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<P class="indent10 NormalText">Description of <A HREF="___">resource</A> text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text.</P>
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 09 March 2016</SPAN></TD>
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