326 lines
16 KiB
HTML
326 lines
16 KiB
HTML
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
<!-- PubChem template version 5.1 2012-05 -->
|
|
<!-- $Id: about.html 367034 2012-06-20 14:44:12Z jiazhang $ -->
|
|
<html xmlns="http://www.w3.org/1999/xhtml">
|
|
<head xmlns:xi="http://www.w3.org/2001/XInclude">
|
|
<meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
|
|
<meta name="description" content="Quick start (How To) guides for using the Molecular Modeling Database (MMDB), a resource of the National Center for Biotechnology Information (NCBI) Structure Group" />
|
|
<meta name="ncbi_db" content="pubchem" />
|
|
<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" />
|
|
<meta name="robots" content="index,follow,noarchive" />
|
|
<title>How To Use the Molecular Modeling Database (MMDB)</title>
|
|
<script type="text/javascript" src="/Structure/scripts/loadbasics.min.js"></script>
|
|
<script type="text/javascript" src="/Structure/scripts/doc_tmp.min.js"></script>
|
|
<link rel="stylesheet" type="text/css" href="/Structure/stylesheets/struct_style_subset.min.css">
|
|
<!-- ========== BEGIN_GOVT_SHUTDOWN_NOTICE_added_20130927 =========== -->
|
|
|
|
<script type="text/javascript">
|
|
jQuery.getScript("/core/alerts/alerts.js", function () {
|
|
galert(['div#governmentshutdown', 'body > *:nth-child(1)'])
|
|
});
|
|
</script>
|
|
|
|
<!-- ========== END_GOVT_SHUTDOWN_NOTICE_added_20130927 =========== -->
|
|
</head>
|
|
|
|
<body>
|
|
<A NAME="Top"></A>
|
|
<A NAME="top"></A>
|
|
|
|
<!-- ======= BEGIN_GET_PUBCHEM_HEADER_AND_NCBILOCALNAV_PULLDOWN_MENUS ========= -->
|
|
<script type="text/javascript">doc_tmp.getDocHdr('structure');</script>
|
|
<!-- ======= END_GET_PUBCHEM_HEADER_AND_NCBILOCALNAV_PULLDOWN_MENUS ========= -->
|
|
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell MiniText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ==================== END_VERTICAL SPACER ======================= -->
|
|
|
|
|
|
<!-- ##################### BEGIN_EDITABLE_CONTENT ##################### -->
|
|
<A NAME="3"></A>
|
|
|
|
<!-- ######### BEGIN_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT ######## -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCell">
|
|
|
|
<!-- ==================== TITLE_OF_DOCUMENT =================== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
|
|
<TD class="DocTitleText" align="left"> 3D Macromolecular Structures</TD>
|
|
|
|
<!-- ===================== GREEN_BUTTONS ====================== -->
|
|
|
|
<TD width="300" bgcolor="#FFFFFF">
|
|
|
|
<TABLE width="300" border="0" style="border-collapse:separate;" cellspacing="1" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../mmdb.shtml"> OVERVIEW </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="mmdb_search.html"> SEARCH </A></TD>
|
|
|
|
<TD class="NavResourceButtonActive" align="center" valign="center" style="white-space: nowrap;"><A href="mmdb_how_to.html"> HOW TO </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="mmdb_help.html"> HELP </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="mmdb_news.html"> NEWS </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="//ftp.ncbi.nih.gov/mmdb"> FTP </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="macromol_publications.html"> PUBLICATIONS </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../../structure_discover.html"> DISCOVER </A></TD>
|
|
|
|
<TD class="WhiteCell" width="1"> </TD>
|
|
<TR>
|
|
</TABLE>
|
|
|
|
</TD>
|
|
|
|
<!-- =================== END_GREEN_BUTTONS ==================== -->
|
|
|
|
<TD class="MiniText" width="5"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell MicroText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================= CONTENT_AREA ==================== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
|
|
<!-- ================= LEFT_SIDE_CONTENT_AREA ================== -->
|
|
|
|
<TD class="WhiteCellWithPadding" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<!-- ======================== BOX1 =========================== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">How to use the Molecular Modeling Database (MMDB) and related resources: examples</TD>
|
|
</TR>
|
|
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell ThumbText" ALIGN="Center" VALIGN="TOP">
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell ThumbText">
|
|
<TR>
|
|
<TD class="WhiteCell" WIDTH="50" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCellBlueEdgeAll" ALIGN="CENTER" VALIGN="TOP">
|
|
<SPAN class="MiniText"> <BR></SPAN>
|
|
<P class="indent20bottomspace ThumbText2">This page provides <B>quick start guides</B> for some common types of searches.<BR>The <a href="mmdb_help.html"><B>MMDB Help document</B></a> provides additional search tips. <!-- 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>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="50" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<!-- P class="indent10"><A HREF="mmdb_how_to_search_by_gene.html"><B>Retrieve structures for a gene/protein product of interest</B></A></P><BR><BR -->
|
|
|
|
<A NAME="SearchMMDB"></A>
|
|
<P class="indent10"><B>Retrieve specific subsets of resolved structures</B></P>
|
|
|
|
<UL>
|
|
<LI><A HREF="mmdb_how_to_search_by_gene.html">Find <B>structures for a gene/protein product of interest</B>.</A></LI>
|
|
<LI><A HREF="mmdb_how_to_search_by_chemical.html">Find 3D structures bound to a <B>specific chemical</B> (e.g., aspirin).</A></LI>
|
|
<LI><A HREF="mmdb_how_to_search_by_small_biopolymer.html">Find 3D structures bound to a <B>specific small biopolymer</B> (e.g., a peptide).</A></LI>
|
|
<LI><A HREF="mmdb_how_to_search_by_molecule_type.html">Retrieve 3D structures for a <B>specific type of molecule</B>, such as protein, RNA, DNA, protein+chemical, etc.</A></LI>
|
|
<LI><A HREF="mmdb_how_to_search_by_taxon.html">Retrieve all structures from a <B>particular source organism or taxon</B>.</A></LI>
|
|
</UL>
|
|
|
|
<A NAME="CBLASTRelatedStructures"></A>
|
|
<P class="indent10"><B>Find structural templates for proteins</B></P>
|
|
|
|
<UL>
|
|
<LI><A HREF="mmdb_how_to_align_query_protseq_to_struct.html"><B>Align a query protein to a similar sequence from a 3D structure</B> and interactively view sequence/structure relationships</A>.</LI>
|
|
<!-- LI><A HREF="___">Find a structural template for a <B>protein sequence that does not yet have a resolved structure</B>.</A></LI>
|
|
<LI><A HREF="___">Find a structural template for a <B>conserved domain</B> within your protein sequence of interest.</A></LI>
|
|
<LI><A HREF="___">ALT: Retrieve <B>structures for the protein encoded by a gene of interest</B>. If a resolved structure does not yet exist for that specific protein, retrieve structures for similar protein sequences.</A></LI -->
|
|
</UL>
|
|
|
|
<A NAME="VAST"></A>
|
|
<P class="indent10"><B>Find structures that are similar in 3D shape</B> (using <!-- the Vector Alignment Search Tool: --> <A HREF="../../VAST/vast.shtml"><B>VAST</B></A>)</P>
|
|
|
|
<UL>
|
|
<LI><A HREF="mmdb_how_to_find_similar_structures.html">Find structures with <B>similarly shaped proteins or 3D domains</B>, regardless of their degree of sequence similarity.</A> [<A HREF="../../VAST/vast.shtml">VAST</A>]</LI>
|
|
<LI><A HREF="mmdb_how_to_find_similar_structures_biounits.html">Find structures with <B>similarly shaped biological assemblies</B>, regardless of their degree of sequence similarity.</A> [<A HREF="../../vastplus/vastplus.cgi">VAST+</A>]</LI>
|
|
<LI><A HREF="mmdb_how_to_use_vastsearch.html">Compare a <B>newly resolved 3D structure in PDB format</B> against the 3D coordinates of known structures already in the public domain.</A> [<A HREF="../../VAST/vastsearch.html">VAST Search</A>]</LI>
|
|
</UL>
|
|
|
|
<A NAME="Cn3D"></A>
|
|
<P class="indent10"><B>View 3D structures</B></P>
|
|
|
|
<UL>
|
|
<LI><A HREF="mmdb_how_to_view_in_cn3d.html">Interactively view a 3D structure and its corresponding sequence data to <B>examine sequence-structure relationship</B>.<!-- Highlight residues in either the 3D structure or the sequence alignment to see their location in both views. --></A></LI>
|
|
<LI><A HREF="mmdb_how_to_view_active_site_residues.html">Identify putative <B>active site</B> residues.</A></LI>
|
|
<!-- LI><A HREF="mmdb_how_to_view_active_site_residues.html">Identify the amino acids that appear to be involved in an <B>active site</B>.</A></LI -->
|
|
<!-- LI><A HREF="mmdb_how_to_display_vast_neighbors_superposed.html">Display a <B>superposition of two or more similiar structures</B> along with their corresponding sequence alignment.</A></LI -->
|
|
</UL>
|
|
|
|
<!-- P class="indent10"><A HREF="___"><B>Section N</B></A></P>
|
|
|
|
<UL>
|
|
<LI><A HREF="___">description with key terms in <B>bold face</B> text text text.</A></LI>
|
|
<LI><A HREF="___">description with key terms in <B>bold face</B> text text text.</A></LI>
|
|
<LI><A HREF="___">description with key terms in <B>bold face</B> text text text.</A></LI>
|
|
</UL -->
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell MiniText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell ThumbText" ALIGN="Center" VALIGN="TOP">
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell ThumbText">
|
|
<TR>
|
|
<TD class="WhiteCell" WIDTH="20" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell" ALIGN="LEFT" VALIGN="TOP">
|
|
<P class="indent20bottomspace ThumbText2">* This page provides <B>quick start guides</B> for some common types of searches.<BR> 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>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="20" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
</TD>
|
|
</TR -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell MiniText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX1 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE -->
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
</TD>
|
|
|
|
<!-- ================= END_LEFT_SIDE_CONTENT_AREA ==================== -->
|
|
|
|
|
|
<!-- =================== RIGHT_SIDE_CONTENT_AREA ================ -->
|
|
|
|
<!-- TD WIDTH="300" class="Yellow1CellBlueEdge" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">Box 5 Header</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="Yellow1Cell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<BR><BR>
|
|
|
|
</TD -->
|
|
|
|
|
|
<!-- ======= SPACER_COLUMN_TO_RIGHT_OF_CONTENT_AREA ========= -->
|
|
|
|
<!-- TD class="WhiteCell" width="1"></TD -->
|
|
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- =========== PAGE_MARGIN_TO_RIGHT_OF_CONTENT_AREA =============== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############ END_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT_AND_TOC ######## -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ==================== END_VERTICAL SPACER ======================= -->
|
|
|
|
<!-- =================== PAGE_FOOTER_AND_DATE_REVISED ================== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 23 September 2016</SPAN></TD>
|
|
<TD width="25"><IMG SRC="/coreweb/template1/pix/pixel.gif" width="1" height="1" alt="" border=0></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- =================== END_PAGE_FOOTER_AND_DATE_REVISED ================== -->
|
|
|
|
|
|
<!-- ##################### END_EDITABLE_CONTENT ##################### -->
|
|
|
|
<script type="text/javascript">doc_tmp.getDocFtr('<A HREF="/research/">Computational Biology Branch</A> > <A HREF="/Structure/index.shtml">Structure Group</A> > <A HREF="/Structure/MMDB/mmdb.shtml">Macromolecular Structures</A> > How To','other');</script>
|
|
|
|
<!-- script type="text/javascript">doc_tmp.getDocFtr(' > <A HREF="______">__________</A> > <A HREF="______">__________</A> > <A HREF="______">__________</A> > ___currentpage_____', 'other');</script -->
|
|
|
|
</body>
|
|
</html>
|