493 lines
22 KiB
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493 lines
22 KiB
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<meta name="description" content="NRPDB: A non-redundant PDB data set for the 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>nr-PDB: Non-redundant PDB data set for VAST</title>
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<TD class="DocTitleText" align="left"> <A HREF="../vast.shtml">VAST: <SPAN class="DocTitleTextSmall13">Vector Alignment Search Tool</SPAN></A></TD>
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<!-- the contents -->
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<!-- =================== BEGIN_EDITABLE_CONTENT_AREA ================ -->
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<!-- ================= CONTENT_AREA_ROW_1 ================== -->
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<!-- =================== BOX1_INTRO_AND_FORMS ======================= -->
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<!-- ########## BLUE_HEADER ########## -->
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<TR>
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP"><B>Non-redundant PDB chain set</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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<TR>
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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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<SPAN class="ThumbText2"><B>The Non-redundant PDB chain set</B></SPAN> gives you a set of sequence-dissimilar PDB polypeptide chains. It is derived by clustering chains into groups according to their amino acid sequence similarities and selecting a representative from each of those groups. (See below for <A href="#details">details</A> of the method).<BR><BR>
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Four sets of chains of different non-redundancy are available. They are based on the clustering using four different sequence-similarity cutoffs: <A href="https://blast.ncbi.nlm.nih.gov/">BLAST</A> p-value of 10e-7, 10e-40, 10e-80, and 100% sequence identity (see <A href="#details">below</A>). The set based on the p-value cutoff of 10e-7 is the most non-redundant one. The one based on 100% sequence identity simply gives a set of all chains with different sequences.<BR><BR>
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Below, you can browse the non-redundant set, or browse clusters of sequence-similar chains from each of which one chain was selected to enter into the non-redundant set. You can also download an ASCII text file that summarizes the non-redundant PDB chain set.<BR><BR>
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<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
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<!-- =========== REPRESENTATIVES =============== -->
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<H3>Representatives</H3>
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<P CLASS="indent40">
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This lists a set of sequence-dissimilar chains (non-redundant set):
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<FORM method="post" action="nrpdbsrv.cgi">
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<TABLE style="margin:0px 0px 0px 0px;" border=0 width=70%>
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<TR valign="top">
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<TD class="NormalText" align="left"> </TD>
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<TD class="NormalText" align="left"><B>Non-redundancy</B></TD>
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<TD class="NormalText" align="left"><B>Display</B></TD>
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</TD>
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<TD align="left">
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<SELECT name="nrlevel">
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<OPTION value=0 selected>p-value 10e-7
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<OPTION value=1>p-value 10e-40
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<OPTION value=2>p-value 10e-80
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<OPTION value=3>non-identical
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</SELECT>
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</TD>
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<TD align="left" valign="top">
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<SELECT name="ltable">
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<OPTION value="long" selected>Details
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<OPTION value="short">PDB codes only
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</SELECT>
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</TD>
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</FORM>
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<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
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</TR>
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<!-- =========== CLUSTER_OF_SEQUENCE_SIMILAR_CHAINS =============== -->
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<TR>
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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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<H3>Cluster of Sequence-Similar Chains</H3>
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<P CLASS="indent40">
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This shows a cluster of sequence-similar chains to which the query PDB chain belongs and from which a representative is selected to enter into the non-redundant set:
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<FORM method="post" action="nrpdbsrv.cgi">
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<TABLE style="margin:0px 0px 0px 0px;" border=0>
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<TR valign="top">
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<TD class="NormalText" align="left">Non-redundancy</TD>
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<TD class="NormalText" align="left">Query</TD>
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<TD class="NormalText" align="left"> </TD>
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</TR>
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<TR valign="top">
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<TD align="left" valign="top">
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<SELECT name="nrlevel">
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<OPTION value=0 selected>p-value 10e-7
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<OPTION value=1>p-value 10e-40
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<OPTION value=2>p-value 10e-80
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<OPTION value=3>non-identical
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</SELECT>
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</TD>
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<TD class="NormalText" align="left" valign="top">
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<B>PDB code</B>
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<INPUT type="text" name="pdbcode" size=6>
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<BR>
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<B>chain id</B>
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<INPUT type="text" name="chainid" size=2>
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</TD>
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<TD class="NormalText" align="left">
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<B><INPUT type="submit" name="group" value="Show "></B>
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<BR>
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<INPUT type="reset" value="Reset">
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</td>
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</TABLE>
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</FORM>
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</P>
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</TD>
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<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
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</TR>
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<!-- =========== DOWNLOAD_SUMMARY_TABLE =============== -->
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<TR>
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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="ftp://ftp.ncbi.nih.gov/mmdb/nrtable/"><H3>Download Summary Table</H3></A>
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<P CLASS="indent40">
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<!-- ORIGINAL TEXT: This gives you an ASCII text file that summarizes the non-redundant sets.<BR><BR -->
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You can download an ASCII text file that summarizes the non-redundant sets present in the current MMDB release or previous releases from the MMDB FTP site:<BR><BR>
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<!-- The MMDB FTP site provides ASCII text files that summarize the non-redundant sets present in the current and previous MMDB releases.<BR><BR -->
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<A href="ftp://ftp.ncbi.nih.gov/mmdb/nrtable/">ftp://ftp.ncbi.nih.gov/mmdb/nrtable/</A>
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</P>
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<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
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<!-- =========== ______________ =============== -->
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<H3>______________</H3>
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Text text text text...<BR><BR>
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Text text text text...<BR><BR>
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<!-- =========== IMAGE =============== -->
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<img src="________.png" width="500" height="100"><BR><BR>
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<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
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<BR> <BR></TD>
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</TABLE>
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<!-- ================= END_BOX1_INTRO_AND_FORMS ===================== -->
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<!-- ============ VERTICAL_SPACER_WITHIN_CONTENT_AREA ============= -->
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<!-- ==================== VERTICAL SPACER ======================= -->
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<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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<!-- ================== END_VERTICAL SPACER ===================== -->
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<!-- =================== BOX2_METHOD_DETAILS ======================= -->
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<A NAME="details"></A><A NAME="Details"></A>
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<A NAME="method"></A><A NAME="Method"></A>
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<!-- ########## BLUE_HEADER ########## -->
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP"><B>Method for making the non-redundant set</B></TD>
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<!-- ########## END_BLUE_HEADER ########## -->
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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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All the chains available from PDB are compared with each other using the <A href="https://blast.ncbi.nlm.nih.gov/">BLAST</A> algorithm as implemented in the <A href="ftp://ftp.ncbi.nih.gov/toolbox/">NCBI toolkit library</A>. They are then clustered into groups of sequence-similar chains using the single-linkage clustering procedure. Chains within a sequence-similar group thus derived are automatically ranked according to the precision and completeness of their structural data. The following measures of the structural quality are used in this order of priority:<BR><BR>
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<OL>
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<LI>Lower percentage of residues with unknown amino acid type,</LI>
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<LI>Lower percentage of residues with incomplete coordinate data,</LI>
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<LI>Lower percentage of residues whose coordinate data are missing,</LI>
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<LI>Lower percentage of residues with incomplete side-chain coordinate data,</LI>
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<LI>Higher resolution,</LI>
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<LI>Larger number of chains (subunits) contained in the PDB entry,</LI>
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<LI>Larger number of heterogens contained in the PDB entry,</LI>
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<LI>Larger number of different types of heterogens,</LI>
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<LI>Larger number of residues, and</LI>
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<LI>Alphanumerical order of their PDB codes.</LI>
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</OL>
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The top-ranked chain is generally chosen as the representative of the group. In some cases, however, a lower-ranked chain may be chosen by the authors manually. For example, if the top-ranked chain was a mutant protein and there was a native protein with reasonably comparable structural quality, then that lower-ranked native protein might replace the mutant. Representatives from all the groups together form a non-redundant set.<BR><BR>
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In comparing sequences, the database-size parameter of the BLAST algorithm is fixed at 500,000. This allows the use of the constant p-value cutoffs in clustering chains. In clustering chains, four different similarity cutoffs are used. They are: BLAST p-values of 10e-7, 10e-40, 10e-80, and 100% sequence identity. This results in a hierarchical clustering of PDB chains and four sets of representatives of different non-redundancy.<BR><BR>
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The non-redundant set does not include chains with less than 20 residues or chains whose coordinates are a theoretical model. A chain with more than 5% "UNKNOWN" residues is included in the clustering but will not be selected as a representative.<BR><BR>
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The non-redundant set is updated on a regular basis (about once a month), in synchronization with updates of MMDB and the VAST database of structure neighbors.<BR>
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</TD>
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<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
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</TR>
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<!-- =========== ______________ =============== -->
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<!-- TR>
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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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<H3>______________</H3>
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<P CLASS="indent40">
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Text text text text...<BR><BR>
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Text text text text...<BR><BR>
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</P>
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<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
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</TR -->
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<!-- =========== IMAGE =============== -->
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<!-- TR>
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<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
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<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
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<img src="________.png" width="500" height="100"><BR><BR>
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</TD>
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<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
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</TR -->
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</TABLE>
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</TD>
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</TR>
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<TR>
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<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
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<BR> <BR></TD>
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</TR>
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</TABLE>
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<!-- ================ END_BOX2_METHOD_DETAILS ===================== -->
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</TD>
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<!-- ============== END_CONTENT_AREA_ROW_1_CELL_1 ================= -->
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</TR>
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</TABLE>
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<!-- ============== END_CONTENT_AREA_ROW_1 ================= -->
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<!-- ===== VERTICAL_SPACER_SEPARATING_ROW_1_and_ROW_2 ===== -->
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<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD class="WhiteCell MiniText"> </TD>
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</TR>
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</TABLE -->
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<!-- ================== END_VERTICAL SPACER ===================== -->
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<!-- ==================== VERTICAL SPACER ======================= -->
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<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD class="WhiteCell NormalText"> </TD>
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</TR>
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</TABLE>
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<!-- ================== END_VERTICAL SPACER ===================== -->
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<!-- ############ END_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT ######## -->
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<!-- =================== PAGE_FOOTER_AND_DATE_REVISED ================== -->
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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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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</TR>
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</TABLE>
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<!-- =================== END_PAGE_FOOTER_AND_DATE_REVISED ================== -->
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<!-- ##################### END_EDITABLE_CONTENT ##################### -->
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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> > <A HREF="https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml">VAST</A> > nrPDB','other');</script>
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<!-- script type="text/javascript">doc_tmp.getDocFtr(' > <A HREF="______">__________</A> > <A HREF="______">__________</A> > <A HREF="______">__________</A> > ___currentpage_____', 'other');</script -->
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</body>
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</html>
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