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<B>How to compare a newly resolved 3D structure in PDB format against the 3D coordinates of structures in MMDB</B></TD>
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<P class="indent20bottomspace NormalText3">Prefatory text and <A HREF="#___">link</A>, if applicable text text text text text text text text text text text text text text text text text text 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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If you have the 3D coordinates of a structure in <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB format</A>, you can use the <A HREF="/Structure/VAST/vastsearch.html">VAST Search</A> tool to compare your structure against those in the <A HREF="/sites/entrez?db=structure">Entrez Structure</A> database (also known as the Molecular Modeling Database, "MMDB") in order to find similar 3D structures:</P>
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<BLOCKQUOTE>
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<UL>
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<LI>Upload your <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB format</A> structure file into the <A HREF="/Structure/VAST/vastsearch.html">VAST Search</A> tool.</LI><BR><BR>
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<LI>VAST Search results will parse your data file and present a summary of the protein chains and <A HREF="mmdb_help.html#DataProcessing3dDomains"><B>3D domains</B></A> present in your structure (<A HREF="../../VAST/vasthelp.html#VASTMoleculeList"><span style="color:#d70000">illustrated example</span></A>). At this point, you can use the <B>View 3D Structure</B> button to interactively view your structure and the corresponding sequence data in the <A HREF="/Structure/CN3D/cn3d.shtml"><B>Cn3D</B></A> program, or the <B>Start</B> button to begin the VAST calculation.</LI><BR><BR>
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<LI>If you press the Start button, the VAST search results page will list the 3D structures that are geometrically similar to all or part of each protein chain in your query structure (<A HREF="../../VAST/vasthelp.html#VASTGraph"><span style="color:#d70000">illustrated example</span></A>). The <B>List</B> options at the top of the VAST Search results page allow you to control the number of VAST hits you see. Because the number of hits can be large, only a "medium <A HREF="../../VAST/vasthelp.html#VASTNR">redundancy</A>" subset of hits is shown by default; you can change the "List" option to view <B>All Sequences</B>, if desired.</LI><BR><BR>
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<LI>Use the check boxes to select hits of interest and press the <B>View 3D Alignment</B> button to view your structure superposed onto the selected structures in Cn3D, along with a corresponding sequence alignment (<A HREF="../../VAST/vast.shtml#Illustration"><span style="color:#d70000">illustrated example</span></A>). (In order for the "View 3D Alignment" button to work, the <A HREF="/Structure/CN3D/cn3d.shtml"><B>Cn3D</B></A> program must be present on your computer. It is a free helper application available for Windows, Macintosh, and Unix platforms. Installation takes only a couple of minutes and a <A HREF="/Structure/CN3D/cn3dtut.shtml"><B>tutorial</B></A> describes the program's features and functions.)</LI><BR><BR>
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</BLOCKQUOTE>
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<IMG src="images/____.png" height="150" width="500" border="1" align="left" alt="Illustration of ___________.">
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 23 September 2016</SPAN></TD>
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