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<meta name="description" content="Vector Alignment Search Tool (VAST), which uses purely geometric criteria to find similar 3D macromolecular structures and identify distant homologs that cannot be recognized by sequence comparison alone. Developed by the National Center for Biotechnology Information's Structure Group." />
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<meta name="keywords" content="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), VAST+, Conserved Domains Database (CDD), CDTree, CD Tree, PubChem, NCBI, National Center for Biotechnology Information" />
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<title>VAST: Vector Alignment Search Tool</title>
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<!-- ==================== VERTICAL SPACER ======================= -->
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<TD class="DocTitleText" align="left"> <A HREF="vast.shtml"><B>VAST: </B><SPAN class="DocTitleTextSmall13"><B>Vector Alignment Search Tool</B></SPAN></A></TD>
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<!-- ===================== GREEN_BUTTONS ====================== -->
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<TD class="NavResourceButtonActive" align="center" valign="center" style="white-space: nowrap;"><A href="vast.shtml"> ABOUT </A></TD>
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<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../MMDB/docs/mmdb_how_to.html#VAST"> HOW TO </A></TD -->
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="vastsearch.html"> SEARCH </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="vasthelp.html"> HELP </A></TD>
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<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="vastsrchelp.html"> VAST SEARCH HELP </A></TD -->
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<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../vastplus/docs/vastplus_help.html"> VAST+ HELP </A></TD -->
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="nrpdb.html"> nr-PDB </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="docs/vast_publications.html"> PUBLICATIONS </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A HREF="../MMDB/mmdb.shtml" title="Overview of macromolecular resources available from the NCBI Structure Group"> RESOURCES </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../MMDB/docs/mmdb_news.html" title="News about the macromolecular resources available from the NCBI Structure Group"> NEWS </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A HREF="../structure_discover.html" title="Discover associations among protein sequence, function, and structure"> DISCOVER </A></TD>
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP"><B>About VAST</B></TD>
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</TR>
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<!-- ########## END_BLUE_HEADER ########## -->
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<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
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<!-- =============== INTRO =================== -->
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<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
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<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
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<!-- A HREF="vast.shtml" --><B>VAST</B>, short for <B>V</B>ector <B>A</B>lignment <B>S</B>earch <B>T</B>ool<!-- /A -->, is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures ("<B>similar structures</B>") by <B>purely geometric criteria</B>, and to identify distant homologs that cannot be recognized by sequence comparison.<BR>
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<TABLE style="margin:0px 0px 0px 0px;" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="5" BGCOLOR="#FFFFFF">
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<TD CLASS="WhiteCell" COLSPAN="3"><img SRC="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif" width="25" height="5" border="0"></TD>
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<TD WIDTH="200" CLASS="IceBlueCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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<img SRC="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif" width="25" height="2" border="0"><br>
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<A HREF="#RetrievePrecomputedResults"><span style="color:#0066CC">Find similarly shaped<br>individual protein molecules<br>or 3D domains<!-- br>(Original VAST) --></SPAN></A></TD>
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<TD WIDTH="10" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD WIDTH="___" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
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<A HREF="vasthelp.html#IllustrationLipocalins"><IMG SRC="docs/images/lipocalin_ecoli_2ACOB_tabacco_hornworm_1Z24A_human_2HZQA_thumbnail.png" WIDTH="150" HEIGHT="150" BORDER="0" ALIGN="RIGHT" ALT="Example 3D alignment of VAST similar structures, showing the ancient evolutionary relationship among lipocalins from bacteria, insects, and human. Click on the image to view the enlarged, annotated version at the bottom of this page."></A>
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<IMG SRC="../IMG/spacer.gif" width="20" height="150" border="0" align="right">
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The <A HREF="vasthelp.html#OriginalVASTDisplay"><B>original VAST</B></A> finds structures that are 3D similar to <B>individual protein molecules</B>, or individual <A HREF="../MMDB/docs/mmdb_help.html#DataProcessing3dDomains"><B>3D domains</B></A>. The original-style VAST display can be viewed by clicking on the <!-- A HREF="../vastplus/docs/vastplus_help.html#OriginalVAST" --><B>"Original VAST" button</B><!-- /A --> on any VAST+ search results page.<!-- (By default, the newer style VAST+ results are displayed when you <A HREF="#RetrievePrecomputedResults">retrieve pre-computed results</A> for structures that are available in MMDB, and the original VAST results are one click away.) -->
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The <A HREF="vasthelp.html">original VAST help document</A> provides an <span style="color:#d70000"><I>illustrated examples</I></span> of original style <A HREF="vasthelp.html#OriginalVAST">VAST search results</A>, <A HREF="vasthelp.html#VASTGraph">alignment footprints</A>, and an example <A HREF="vasthelp.html#IllustrationLipocalins">3D superposition</A> of lipocalins from bacteria, insect, and human. 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"><I>illustrated examples</I></span> of the newer VAST+ search results</A>, where you can see the "Original VAST" button near the upper right corner of each illustration, and summarizes the <A HREF="../vastplus/docs/vastplus_help.html#Compare">difference between VAST and VAST+</A>. <A HREF="docs/vast_publications.html">Publications</A> provide additional details about both.</TD>
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<TD CLASS="WhiteCell" COLSPAN="3"><img SRC="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif" width="25" height="5" border="0"></TD>
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<TD WIDTH="200" CLASS="IceBlueCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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<img SRC="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif" width="25" height="2" border="0"><br>
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<A HREF="../vastplus/vastplus.cgi"><span style="color:#0066CC">Find similarly shaped<br>macromolecular complexes<!-- br>(VAST+) --></SPAN></A></TD>
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<TD WIDTH="10" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD WIDTH="___" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
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<A HREF="../vastplus/docs/vastplus_help.html#IllustratedExample1B26"><IMG SRC="../vastplus/docs/images/1b26_vastplus_neighbor_1GTM_thumbnail.png" WIDTH="150" HEIGHT="130" BORDER="0" ALIGN="RIGHT" ALT="Example VAST+ similar structures, showing the interaction schematics of glutamate dehydrogenase molecular complexes from Thermotoga maritima and Pyrococcus furiosus. Click on the image to view the enlarged, annotated version in the VAST+ help document."></A>
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<IMG SRC="../IMG/spacer.gif" width="20" height="130" border="0" align="right">
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An <B>enhanced resource</B>, <A HREF="../vastplus/vastplus.cgi"><B>VAST+</B></A>, finds structures that are 3D similar to your query structure's <B>macromolecular complex</B> (<A HREF="../vastplus/docs/vastplus_help.html#OutputBiologicalUnit">biological unit</A>). The search form in the "<A HREF="#RetrievePrecomputedResults">Retrieve pre-computed results</A>" section of this page, below, will retrieve VAST+ results for the query structure that you specify.
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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"><I>illustrated examples</I></span> of VAST+ search results</A>, featuring similar structures for <A HREF="../vastplus/docs/vastplus_help.html#IllustratedExample1B26">glutamate dehydrogenase</A> (<I>Thermotoga maritima</I>) and <A HREF="../vastplus/docs/vastplus_help.html#IllustratedExample1HBB">deoxyhemoglobin</A> (<I>Homo sapiens</I>). The help document also describes the <A HREF="../vastplus/docs/vastplus_help.html#Compare">difference between VAST and VAST+</A>.<!-- The <A HREF="../vastplus/docs/vastplus_help.html">VAST+ help document</A> provides additional details, including <I><A HREF="../vastplus/docs/vastplus_help.html#IllustratedExamples"><span style="color:#d70000">illustrated examples</span></A></I> of search results for <A HREF="../vastplus/docs/vastplus_help.html#IllustratedExample1B26">glutamate dehydrogenase (<I>Thermotoga maritima</I>)</A> and <A HREF="../vastplus/docs/vastplus_help.html#IllustratedExample1HBB">deoxyhemoglobin (<I>Homo sapiens</I>)</A>. -->
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<TD WIDTH="200" CLASS="IceBlueCell NormalText" ALIGN="LEFT" VALIGN="TOP"><A NAME="RetrievePrecomputedResults"></A><!-- A HREF="#RetrievePrecomputedResultsSearchForm" --><span style="color:#0066CC">Retrieve pre-computed results</SPAN></TD>
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<TD WIDTH="10" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD WIDTH="___" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
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<table border="0" width="100%" cellspacing="0" cellpadding="0" class="NormalText">
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<td valign="top">
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VAST and VAST+ are applied on every protein in the <A HREF="https://www.ncbi.nlm.nih.gov/structure/">Molecular Modeling Database (MMDB)</A> during <A HREF="../MMDB/docs/mmdb_help.html#DataProcessingGeometricalFeatures">MMDB data processing</A> in order to identify similar 3D structures.<BR><BR>
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To retrieve the <B>pre-computed results</B>, follow the "<B>Similar Structures</B>" link on a <A HREF="../MMDB/docs/mmdb_help.html#SummaryPage">structure's summary page</A> or use any of the <A HREF="vasthelp.html#VASTHow">access methods</A> described in the <A HREF="vasthelp.html">VAST help document</A><!--, or simply enter your query structure's <A HREF="../MMDB/docs/mmdb_help.html#MmdbsrvMMDBID">MMDB ID</A> or <A HREF="../MMDB/docs/mmdb_help.html#MmdbsrvPDBID">PDB ID</A> below and press "GO."--> <BR><BR>
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<!--A NAME="RetrievePrecomputedResultsSearchForm"></A>
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<table border="0" width="100%" cellspacing="0" cellpadding="0" class="NormalText">
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<td class="NormalText" align="LEFT">
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<FORM METHOD="post" ACTION="/Structure/vastplus/vastplus.cgi">
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<B>Show Similar Structures for:</B>
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<INPUT TYPE="text" NAME="uid" SIZE=15 placeholder="PDB ID or MMDB ID">
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<INPUT TYPE="hidden" NAME="style" VALUE="old">
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<INPUT TYPE="submit" NAME="submit" VALUE="Go">
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<INPUT TYPE="reset" NAME="reset" VALUE="Clear">
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</FORM>
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</table>
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<BR> -->
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When looking up similar structures from a structure summary page, the new style <B>VAST+ results</B> are displayed by default. <A HREF="../vastplus/docs/vastplus_help.html#IllustratedExamples"><span style="color:#d70000"><I>Illustrated examples</I></span> of VAST + search results</A> are available in <A HREF="../vastplus/docs/vastplus_help.html">VAST+ help document</A> and in the thumbnail to the right.<!-- for human deoxyhemoglobin (PDB ID: 1HBB). Click on the thumbnail to <A HREF="../vastplus/docs/vastplus_help.html#IllustratedExample1HBB">view the enlarged and annotated <span style="color:#d70000"><I>illustrated example</I></span></A> in the <A HREF="../vastplus/docs/vastplus_help.html">VAST+ help document</A>, where you can also read about the <A HREF="../vastplus/docs/vastplus_help.html#Compare">difference between VAST and VAST+</A> --><BR><BR>
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If you prefer to view the <A HREF="vasthelp.html#OriginalVASTDisplay">original style VAST display</A>, click on the <B>"Original VAST" button</B> on any VAST+ search results page. Read more about the <A HREF="../vastplus/docs/vastplus_help.html#Compare">difference between VAST and VAST+</A>.
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<td width="20"> </td>
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<A HREF="../vastplus/docs/vastplus_help.html#IllustratedExample1HBB"><IMG SRC="../vastplus/docs/images/1HBB_vastplus_search_results_thumbnail.png" WIDTH="150" HEIGHT="300" BORDER="0" ALIGN="RIGHT" ALT="Example VAST+ similar structures, showing an excerpt of the search results for human deoxyhemoglobin (1HBB). Click on the image to view the enlarged, annotated version in the VAST+ help document."></A>
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<TD CLASS="WhiteCell" COLSPAN="3"><img SRC="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif" width="25" height="5" border="0"></TD>
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<img SRC="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif" width="25" height="2" border="0"><br>
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<A NAME="InputPDBFormat"></A>
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<A HREF="vastsearch.html"><span style="color:#0066CC">Search with a new structure<br>(PDB formatted file)</SPAN></A></TD>
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<TD WIDTH="10" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD WIDTH="___" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">
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<A HREF="vastsearch.html"><IMG SRC="docs/images/upload_PDB_formatted_file_4P7A_to_VAST_Search_thumbnail.png" WIDTH="150" HEIGHT="200" BORDER="0" ALIGN="RIGHT" ALT="Schematic image depicting the upload of a newly resolved structure in PDB file format to VAST Search, which finds similarly shaped 3D structures and displays their alignment footprints, with options to view sequence alignments and 3D superpositions. Click on the image to open the VAST Search page."></A>
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<!-- the 3D molecular graphic is from 4P7A, human DNA mismatch repair protein, and the footprints are the medium redundancy VAST Search results -->
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<IMG SRC="../IMG/spacer.gif" width="20" height="130" border="0" align="right">
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If you have a <B>newly resolved protein structure</B> that is not yet in MMDB, you can use the <A HREF="vastsearch.html"><B>VAST Search</B></A> service to <A HREF="vastsrchelp.html#Submission">input</A> your data in <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format"><B>PDB file format</B></A> and compare your structure against all those in MMDB in order to find 3D similar structures. The <A HREF="vasthelp.html">VAST Search Help document</A> provides additional information about using the VAST Search page.<BR><BR>
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Please note that, at this time, <A HREF="vastsearch.html">VAST Search</A> still returns results in the <!-- A HREF="../vastplus/docs/vastplus_help.html#OriginalVASTDisplay" --><A HREF="vasthelp.html#OriginalVASTDisplay">original-style VAST display</A>, which lists structures that have similarities to individual protein molecules and <A HREF="../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domains</A> in your query structure, and allows you to view their sequence alignments and 3D superpositions.<BR><BR>
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The new <A HREF="../vastplus/vastplus.cgi">VAST+</A> search results, which rank similar structures based on their <A HREF="../vastplus/docs/vastplus_help.html#OutputBiologicalUnit">biological unit</A> similarity to the query structure, and provide the ability to view sequence alignments and superpositions of the biological units, are currently calculated only for structures that are available in the public database.<!-- The original style VAST results does not rank results by biological unit similarity. --></TD>
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<TD CLASS="WhiteCell" COLSPAN="3"><img SRC="https://www.ncbi.nlm.nih.gov/Structure/IMG/spacer.gif" width="25" height="5" border="0"></TD>
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<TD WIDTH="200" CLASS="IceBlueCell NormalText" ALIGN="LEFT" VALIGN="TOP"><A HREF="../CN3D/cn3d.shtml"><span style="color:#0066CC">View 3D structures<br>and superpositions</SPAN></A></TD>
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<TD WIDTH="10" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD WIDTH="___" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP">Whether you retrieve the original VAST similar structures from the summary page of a publicly available structure, or through a VAST Search, you can then use the free <A HREF="../CN3D/cn3d.shtml"><B>Cn3D</B> structure viewing program</A> to view a superposition of the query structure and similar structures, as shown in the <A HREF="vasthelp.html#LipocalinsIllustration"><span style="color:#d70000"><I>illustrated example</I></span></A> of lipocalins from bacteria, insects, and human that appears in the <A HREF="vasthelp.html">original VAST help document</A>. Click on that illustration to open the interactive 3D alignment in the free Cn3D program. 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"><B>Cn3D Tutorial</B></A> provides additional details about <A HREF="../CN3D/cn3dtutP4.shtml"><B>viewing structure alignments in Cn3D</B></A>.<!-- For best results, use the newest version of the software, Cn3D 4.3.1. --><BR><BR>
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<I>Note: When you retrieve similar structures using <A HREF="../vastplus/vastplus.cgi">VAST+</A>, rather than the original VAST, the 3D superpositions will open automatically in <A HREF="../icn3d/docs/icn3d_help.html">iCn3D</A>, NCBI's web-based structure viewer, without the need to download/install a separate application.</I>
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<TD WIDTH="___" CLASS="NormalText" ALIGN="LEFT" VALIGN="TOP"><A NAME="Illustration"></A>
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<A HREF="docs/data/lipocalin_ecoli_2ACOB_tabacco_hornworm_1Z24A_human_2HZQA.cn3"><IMG SRC="docs/images/lipocalin_ecoli_2ACOB_tabacco_hornworm_1Z24A_human_2HZQA.png" WIDTH="500" HEIGHT="750" BORDER="0" ALT="Example 3D alignment of VAST similar structures, showing the ancient evolutionary relationship among lipocalins from bacteria, insects, and human. Click on the image to open the interactive 3D alignment in the free Cn3D program. Please note that Cn3D must be installed in your computer in order for the file to open."></A></TD>
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<H3>______________</H3>
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 26 September 2016</SPAN></TD>
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<TD width="25"><IMG SRC="https://www.ncbi.nlm.nih.gov/coreweb/template1/pix/pixel.gif" width="1" height="1" alt="" border=0></TD>
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<script type="text/javascript">doc_tmp.getDocFtr('<A HREF="https://www.ncbi.nlm.nih.gov/research/">Computational Biology Branch</A> > <A HREF="https://www.ncbi.nlm.nih.gov/Structure/index.shtml">Structure Group</A> > <A HREF="https://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml">Macromolecular Structures</A> > VAST','other');</script>
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