521 lines
No EOL
112 KiB
HTML
521 lines
No EOL
112 KiB
HTML
<?xml version="1.0" encoding="utf-8"?>
|
||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
||
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
||
|
||
<head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
||
<!-- AppResources meta begin -->
|
||
<meta name="paf-app-resources" content="" />
|
||
<script type="text/javascript">var ncbi_startTime = new Date();</script>
|
||
|
||
<!-- AppResources meta end -->
|
||
|
||
<!-- TemplateResources meta begin -->
|
||
<meta name="paf_template" content="" />
|
||
|
||
<!-- TemplateResources meta end -->
|
||
|
||
<!-- Logger begin -->
|
||
<meta name="ncbi_db" content="books" /><meta name="ncbi_pdid" content="book-part" /><meta name="ncbi_acc" content="NBK21095" /><meta name="ncbi_domain" content="handbook" /><meta name="ncbi_report" content="record" /><meta name="ncbi_type" content="fulltext" /><meta name="ncbi_objectid" content="" /><meta name="ncbi_pcid" content="/NBK21095/" /><meta name="ncbi_pagename" content="Macromolecular Structure Databases - The NCBI Handbook - NCBI Bookshelf" /><meta name="ncbi_bookparttype" content="chapter" /><meta name="ncbi_app" content="bookshelf" />
|
||
<!-- Logger end -->
|
||
|
||
<title>Macromolecular Structure Databases - The NCBI Handbook - NCBI Bookshelf</title>
|
||
|
||
<!-- AppResources external_resources begin -->
|
||
<link rel="stylesheet" href="/core/jig/1.15.2/css/jig.min.css" /><script type="text/javascript" src="/core/jig/1.15.2/js/jig.min.js"></script>
|
||
|
||
<!-- AppResources external_resources end -->
|
||
|
||
<!-- Page meta begin -->
|
||
<meta name="robots" content="NOINDEX,NOFOLLOW,NOARCHIVE,NOIMAGEINDEX" /><meta name="citation_inbook_title" content="The NCBI Handbook [Internet]" /><meta name="citation_title" content="Macromolecular Structure Databases" /><meta name="citation_publisher" content="National Center for Biotechnology Information (US)" /><meta name="citation_date" content="2003/08/13" /><meta name="citation_author" content="Eric Sayers" /><meta name="citation_author" content="Steve Bryant" /><meta name="citation_fulltext_html_url" content="https://www.ncbi.nlm.nih.gov/books/NBK21095/" /><link rel="schema.DC" href="http://purl.org/DC/elements/1.0/" /><meta name="DC.Title" content="Macromolecular Structure Databases" /><meta name="DC.Type" content="Text" /><meta name="DC.Publisher" content="National Center for Biotechnology Information (US)" /><meta name="DC.Contributor" content="Eric Sayers" /><meta name="DC.Contributor" content="Steve Bryant" /><meta name="DC.Date" content="2003/08/13" /><meta name="DC.Identifier" content="https://www.ncbi.nlm.nih.gov/books/NBK21095/" /><meta name="description" content="The resources provided by NCBI for studying the three-dimensional (3D) structures of proteins center around two databases: the Molecular Modeling Database (MMDB), which provides structural information about individual proteins; and the Conserved Domain Database (CDD), which provides a directory of sequence and structure alignments representing conserved functional domains within proteins(CDs). Together, these two databases allow scientists to retrieve and view structures, find structurally similar proteins to a protein of interest, and identify conserved functional sites." /><meta name="og:title" content="Macromolecular Structure Databases" /><meta name="og:type" content="book" /><meta name="og:description" content="The resources provided by NCBI for studying the three-dimensional (3D) structures of proteins center around two databases: the Molecular Modeling Database (MMDB), which provides structural information about individual proteins; and the Conserved Domain Database (CDD), which provides a directory of sequence and structure alignments representing conserved functional domains within proteins(CDs). Together, these two databases allow scientists to retrieve and view structures, find structurally similar proteins to a protein of interest, and identify conserved functional sites." /><meta name="og:url" content="https://www.ncbi.nlm.nih.gov/books/NBK21095/" /><meta name="og:site_name" content="NCBI Bookshelf" /><meta name="og:image" content="https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook-lrg.png" /><meta name="twitter:card" content="summary" /><meta name="twitter:site" content="@ncbibooks" /><meta name="warning" content="This publication is provided for historical reference only and the information may be out of date." /><meta name="bk-non-canon-loc" content="/books/n/handbook/ch3/" /><link rel="canonical" href="https://www.ncbi.nlm.nih.gov/books/NBK21095/" /><link rel="stylesheet" href="/corehtml/pmc/css/figpopup.css" type="text/css" media="screen" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books.min.css" type="text/css" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books_print.min.css" type="text/css" media="print" /><style type="text/css">.main-content {background:transparent repeat-y top left;background-image:url(/corehtml/pmc/css/bookshelf/2.26/img/archive.png);background-size: auto, contain; padding:0 0 0 3em }</style><style type="text/css">p a.figpopup{display:inline !important} .bk_tt {font-family: monospace} .first-line-outdent .bk_ref {display: inline} .body-content h2, .body-content .h2 {border-bottom: 1px solid #97B0C8} .body-content h2.inline {border-bottom: none} a.page-toc-label , .jig-ncbismoothscroll a {text-decoration:none;border:0 !important} .temp-labeled-list .graphic {display:inline-block !important} .temp-labeled-list img{width:100%}</style><script type="text/javascript" src="/corehtml/pmc/js/jquery.hoverIntent.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/common.min.js?_=3.18"> </script><script type="text/javascript" src="/corehtml/pmc/js/large-obj-scrollbars.min.js"> </script><script type="text/javascript">window.name="mainwindow";</script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/book-toc.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/books.min.js"> </script><meta name="book-collection" content="NONE" />
|
||
|
||
<!-- Page meta end -->
|
||
<link rel="shortcut icon" href="//www.ncbi.nlm.nih.gov/favicon.ico" /><meta name="ncbi_phid" content="CE8DF2807DA09761000000000021001D.m_13" />
|
||
<meta name='referrer' content='origin-when-cross-origin'/><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4216699/css/3852956/3985586/3808861/4121862/3974050/3917732/251717/4216701/14534/45193/4113719/3849091/3984811/3751656/4033350/3840896/3577051/3852958/4008682/4207974/4206132/4062871/12930/3964959/3854974/36029/4128070/9685/3549676/3609192/3609193/3609213/3395586.css" /><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4216699/css/3411343/3882866.css" media="print" /></head>
|
||
<body class="book-part">
|
||
<div class="grid">
|
||
<div class="col twelve_col nomargin shadow">
|
||
<!-- System messages like service outage or JS required; this is handled by the TemplateResources portlet -->
|
||
<div class="sysmessages">
|
||
<noscript>
|
||
<p class="nojs">
|
||
<strong>Warning:</strong>
|
||
The NCBI web site requires JavaScript to function.
|
||
<a href="/guide/browsers/#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a>
|
||
</p>
|
||
</noscript>
|
||
</div>
|
||
<!--/.sysmessage-->
|
||
<div class="wrap">
|
||
<div class="page">
|
||
<div class="top">
|
||
<div id="universal_header">
|
||
<section class="usa-banner">
|
||
<div class="usa-accordion">
|
||
<header class="usa-banner-header">
|
||
<div class="usa-grid usa-banner-inner">
|
||
<img src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png" alt="U.S. flag" />
|
||
<p>An official website of the United States government</p>
|
||
<button class="non-usa-accordion-button usa-banner-button" aria-expanded="false" aria-controls="gov-banner-top" type="button">
|
||
<span class="usa-banner-button-text">Here's how you know</span>
|
||
</button>
|
||
</div>
|
||
</header>
|
||
<div class="usa-banner-content usa-grid usa-accordion-content" id="gov-banner-top" aria-hidden="true">
|
||
<div class="usa-banner-guidance-gov usa-width-one-half">
|
||
<img class="usa-banner-icon usa-media_block-img" src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-dot-gov.svg" alt="Dot gov" />
|
||
<div class="usa-media_block-body">
|
||
<p>
|
||
<strong>The .gov means it's official.</strong>
|
||
<br />
|
||
Federal government websites often end in .gov or .mil. Before
|
||
sharing sensitive information, make sure you're on a federal
|
||
government site.
|
||
</p>
|
||
</div>
|
||
</div>
|
||
<div class="usa-banner-guidance-ssl usa-width-one-half">
|
||
<img class="usa-banner-icon usa-media_block-img" src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-https.svg" alt="Https" />
|
||
<div class="usa-media_block-body">
|
||
<p>
|
||
<strong>The site is secure.</strong>
|
||
<br />
|
||
The <strong>https://</strong> ensures that you are connecting to the
|
||
official website and that any information you provide is encrypted
|
||
and transmitted securely.
|
||
</p>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<div class="usa-overlay"></div>
|
||
<header class="ncbi-header" role="banner" data-section="Header">
|
||
|
||
<div class="usa-grid">
|
||
<div class="usa-width-one-whole">
|
||
|
||
<div class="ncbi-header__logo">
|
||
<a href="/" class="logo" aria-label="NCBI Logo" data-ga-action="click_image" data-ga-label="NIH NLM Logo">
|
||
<img src="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/logos/AgencyLogo.svg" alt="NIH NLM Logo" />
|
||
</a>
|
||
</div>
|
||
|
||
<div class="ncbi-header__account">
|
||
<a id="account_login" href="https://account.ncbi.nlm.nih.gov" class="usa-button header-button" style="display:none" data-ga-action="open_menu" data-ga-label="account_menu">Log in</a>
|
||
<button id="account_info" class="header-button" style="display:none" aria-controls="account_popup" type="button">
|
||
<span class="fa fa-user" aria-hidden="true">
|
||
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" width="20px" height="20px">
|
||
<g style="fill: #fff">
|
||
<ellipse cx="12" cy="8" rx="5" ry="6"></ellipse>
|
||
<path d="M21.8,19.1c-0.9-1.8-2.6-3.3-4.8-4.2c-0.6-0.2-1.3-0.2-1.8,0.1c-1,0.6-2,0.9-3.2,0.9s-2.2-0.3-3.2-0.9 C8.3,14.8,7.6,14.7,7,15c-2.2,0.9-3.9,2.4-4.8,4.2C1.5,20.5,2.6,22,4.1,22h15.8C21.4,22,22.5,20.5,21.8,19.1z"></path>
|
||
</g>
|
||
</svg>
|
||
</span>
|
||
<span class="username desktop-only" aria-hidden="true" id="uname_short"></span>
|
||
<span class="sr-only">Show account info</span>
|
||
</button>
|
||
</div>
|
||
|
||
<div class="ncbi-popup-anchor">
|
||
<div class="ncbi-popup account-popup" id="account_popup" aria-hidden="true">
|
||
<div class="ncbi-popup-head">
|
||
<button class="ncbi-close-button" data-ga-action="close_menu" data-ga-label="account_menu" type="button">
|
||
<span class="fa fa-times">
|
||
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 48 48" width="24px" height="24px">
|
||
<path d="M38 12.83l-2.83-2.83-11.17 11.17-11.17-11.17-2.83 2.83 11.17 11.17-11.17 11.17 2.83 2.83 11.17-11.17 11.17 11.17 2.83-2.83-11.17-11.17z"></path>
|
||
</svg>
|
||
</span>
|
||
<span class="usa-sr-only">Close</span></button>
|
||
<h4>Account</h4>
|
||
</div>
|
||
<div class="account-user-info">
|
||
Logged in as:<br />
|
||
<b><span class="username" id="uname_long">username</span></b>
|
||
</div>
|
||
<div class="account-links">
|
||
<ul class="usa-unstyled-list">
|
||
<li><a id="account_myncbi" href="/myncbi/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_myncbi">Dashboard</a></li>
|
||
<li><a id="account_pubs" href="/myncbi/collections/bibliography/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_pubs">Publications</a></li>
|
||
<li><a id="account_settings" href="/account/settings/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_settings">Account settings</a></li>
|
||
<li><a id="account_logout" href="/account/signout/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_logout">Log out</a></li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
</header>
|
||
<div role="navigation" aria-label="access keys">
|
||
<a id="nws_header_accesskey_0" href="https://www.ncbi.nlm.nih.gov/guide/browsers/#ncbi_accesskeys" class="usa-sr-only" accesskey="0" tabindex="-1">Access keys</a>
|
||
<a id="nws_header_accesskey_1" href="https://www.ncbi.nlm.nih.gov" class="usa-sr-only" accesskey="1" tabindex="-1">NCBI Homepage</a>
|
||
<a id="nws_header_accesskey_2" href="/myncbi/" class="set-base-url usa-sr-only" accesskey="2" tabindex="-1">MyNCBI Homepage</a>
|
||
<a id="nws_header_accesskey_3" href="#maincontent" class="usa-sr-only" accesskey="3" tabindex="-1">Main Content</a>
|
||
<a id="nws_header_accesskey_4" href="#" class="usa-sr-only" accesskey="4" tabindex="-1">Main Navigation</a>
|
||
</div>
|
||
<section data-section="Alerts">
|
||
<div class="ncbi-alerts-placeholder"></div>
|
||
</section>
|
||
</div>
|
||
<div class="header">
|
||
<div class="res_logo"><h1 class="res_name"><a href="/books/" title="Bookshelf home">Bookshelf</a></h1><h2 class="res_tagline"></h2></div>
|
||
<div class="search"><form method="get" action="/books/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="books" selected="selected" data-ac_dict="bookshelf-search">Books</option><option value="pmc">PMC</option><option value="nuccore">Nucleotide</option><option value="refseq" class="last">RefSeq</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books" data-ac_dict="bookshelf-search">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search Books. Use up and down arrows to choose an item from the autocomplete." value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="dictionary:'bookshelf-search',disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'no'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div></form><ul class="searchlinks inline_list"><li>
|
||
<a href="/books/browse/">Browse Titles</a>
|
||
</li><li>
|
||
<a href="/books/advanced/">Advanced</a>
|
||
</li><li class="help">
|
||
<a href="/books/NBK3833/">Help</a>
|
||
</li><li class="disclaimer">
|
||
<a target="_blank" data-ga-category="literature_resources" data-ga-action="link_click" data-ga-label="disclaimer_link" href="https://www.ncbi.nlm.nih.gov/books/about/disclaimer/">Disclaimer</a>
|
||
</li></ul></div>
|
||
</div>
|
||
|
||
|
||
|
||
<!--<component id="Page" label="headcontent"/>-->
|
||
|
||
</div>
|
||
<div class="content">
|
||
<!-- site messages -->
|
||
<!-- Custom content 1 -->
|
||
<div class="col1">
|
||
|
||
</div>
|
||
|
||
<div class="container">
|
||
<div id="maincontent" class="content eight_col col">
|
||
<!-- Custom content in the left column above book nav -->
|
||
<div class="col2">
|
||
|
||
</div>
|
||
|
||
<!-- Book content -->
|
||
|
||
|
||
<!-- Custom content between navigation and content -->
|
||
<div class="col3">
|
||
|
||
</div>
|
||
|
||
<div class="document">
|
||
<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>McEntyre J, Ostell J, editors. The NCBI Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2002-. </p></div><div class="bk_msg_box bk_bttm_mrgn clearfix bk_noprnt"><div class="iconblock clearfix"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/handbook2e/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook2e-lrg.png" alt="Cover" height="100px" width="80px" /></a><div class="icnblk_cntnt"><ul class="messages"><li class="info icon"><span class="icon"><a href="/books/n/handbook2e/">See "The NCBI Handbook, 2nd Edition"</a></span></li></ul></div></div></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/handbook/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook-lrg.png" alt="Cover of The NCBI Handbook" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>The NCBI Handbook [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK21095_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK21095_dtls__"><div>McEntyre J, Ostell J, editors.</div><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 2002-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/handbook/">Contents</a></li></ul></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/handbook/ch2/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/handbook/ch4/" title="Next page in this title">Next ></a></div></div></div></div></div>
|
||
<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK21095_"><span class="label">Chapter 3</span><span class="title" itemprop="name">Macromolecular Structure Databases</span></h1><p class="contrib-group"><span itemprop="author">Eric Sayers</span> and <span itemprop="author">Steve Bryant</span>.</p><p class="small">Created: <span itemprop="datePublished">October 9, 2002</span>; Last Update: <span itemprop="dateModified">August 13, 2003</span>.</p><p><em>Estimated reading time: 32 minutes</em></p></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="_abs_rndgid_" itemprop="description"><h2 id="__abs_rndgid__">Summary</h2><p>The resources provided by <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> for studying the three-dimensional (3D) structures of proteins center around two databases: the Molecular Modeling Database (<a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a>), which provides structural information about individual proteins; and the Conserved Domain Database (<a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a>), which provides a directory of sequence and structure alignments representing conserved functional domains within proteins(<a href="/books/n/handbook/A1237/#app18">CD</a>s). Together, these two databases allow scientists to retrieve and view structures, find structurally similar proteins to a protein of interest, and identify conserved functional sites.</p><p>To enable scientists to accomplish these tasks, <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> has integrated <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> and <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> into the <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> retrieval system (<a href="/books/n/handbook/ch15/">Chapter 15</a>). In addition, structures can be found by <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a>, because sequences derived from MMDB structures have been included in the BLAST databases (<a href="/books/n/handbook/ch16/">Chapter 16</a>). Once a protein structure has been identified, the domains within the protein, as well as <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> “neighbors” (i.e., those with similar structure) can be found. For novel data not yet included in Entrez, there are separate search services available.</p><p>Protein structures can be visualized using <a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a>, an interactive 3D graphic modeling tool. Details of the structure, such as ligand-binding sites, can be scrutinized and highlighted. Cn3D can also display multiple sequence alignments based on sequence and/or structural similarity among related sequences, 3D domains, or members of a <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> family. Cn3D images and alignments can be manipulated easily and exported to other applications for presentation or further analysis.</p></div><div id="A95"><h2 id="_A95_">Overview</h2><p>The Structure <a href="/Structure" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">homepage</a> (<a class="figpopup" href="/books/NBK21095/figure/A96/?report=objectonly" target="object" rid-figpopup="figA96" rid-ob="figobA96">Figure 1</a>) contains links to the more specialized pages for each of the main tools and databases, introduced below, as well as search facilities for the Molecular Modeling Database (<a href="/books/n/handbook/A1237/#app112">MMDB</a>; <a class="bk_pop" href="#A236">Ref. 1</a>).
|
||
</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA96" co-legend-rid="figlgndA96"><a href="/books/NBK21095/figure/A96/?report=objectonly" target="object" title="Figure 1" class="img_link icnblk_img figpopup" rid-figpopup="figA96" rid-ob="figobA96"><img class="small-thumb" src="/books/NBK21095/bin/ch3f1.gif" src-large="/books/NBK21095/bin/ch3f1.jpg" alt="Figure 1. The Structure homepage." /></a><div class="icnblk_cntnt" id="figlgndA96"><h4 id="A96"><a href="/books/NBK21095/figure/A96/?report=objectonly" target="object" rid-ob="figobA96">Figure 1</a></h4><p class="float-caption no_bottom_margin">The Structure homepage. This page can be found by selecting the <i>Structure</i> link on the tool bar atop many NCBI Web pages. Two searches can be performed from this page, an Entrez
|
||
<i>Structure</i> search or a Structure <i>Summary</i> search. Both query the MMDB database. <a href="/books/NBK21095/figure/A96/?report=objectonly" target="object" rid-ob="figobA96">(more...)</a></p></div></div><p>
|
||
<a href="/Structure/MMDB/mmdb.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">MMDB</a> is based on the structures within Protein Data Bank (<a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a>) and can be queried using the <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> search engine, as well as via the more direct but less flexible Structure <b>Summary</b> search (see <a class="figpopup" href="/books/NBK21095/figure/A96/?report=objectonly" target="object" rid-figpopup="figA96" rid-ob="figobA96">Figure 1</a>). Once found, any structure of interest can be viewed using <a href="/Structure/CN3D/cn3d.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Cn3D</a> (<a class="bk_pop" href="#A237">2</a>), a piece of software that can be freely downloaded for Mac, PC, and <a href="/books/n/handbook/A1237/#app189">UNIX</a> platforms.</p><p>Often used in conjunction with <a href="/books/n/handbook/A1237/#app27">Cn3D</a> is the Vector Alignment Search Tool (<a href="/books/n/handbook/A1237/#app193">VAST</a>; Refs. <a class="bk_pop" href="#A238">3</a>, <a class="bk_pop" href="#A239">4</a>). <a href="/Structure/VAST/vast.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">VAST</a> is used to precompute “structure neighbors” or structures similar to each <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> entry. For people that have a set of 3D coordinates for a protein not yet in MMDB, there is also a <a href="/Structure/VAST/vastsearch.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">VAST search service</a>. The output of the precomputed VAST searches is a list of structure records, each representing one of the <a href="/Structure/VAST/nrpdb.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Non-Redundant PDB chain</a> sets (<a href="/books/n/handbook/A1237/#app123">nr-PDB</a>), which can also be downloaded. There are four clustered subsets of MMDB that compose <a class="def" href="/books/n/handbook/A1237/def-item/app123/">nr-PDB</a>, each consisting of clusters having a preset level of sequence similarity.</p><p>The structures within <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> are now being linked to the <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> Taxonomy database (<a href="/books/n/handbook/ch4/">Chapter 4</a>). Known as the <a href="/Structure/PDBEAST/pdbeast.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">PDBeast</a> project, this effort makes it possible to find: (1) all MMDB structures from a particular organism; and (2) all structures within a node of the taxonomy tree (such as lizards or <i>Bacillus)</i>, which launches the Taxonomy Browser showing the number of MMDB records in each node.</p><p>The second database within the <b>Structure</b> resources is the Conserved Domain Database (<a href="/books/n/handbook/A1237/#app20">CDD</a>; <a class="bk_pop" href="#A240">Ref. 5</a>), originally based largely on <a href="/books/n/handbook/A1237/#app131">Pfam</a> and <a href="/books/n/handbook/A1237/#app166">SMART</a>, collections of alignments that represent functional domains conserved across evolution. <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> now also contains the alignments of the <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> COG database, the NCBI Library of Ancient Domains (LOAD) along with new curated alignments assembled at NCBI. CDD can be searched from the <a href="/Structure/cdd/cdd.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">CDD</a> page in several ways, including by a <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> keyword search. Three tools have been developed to assist in analysis of CDD: (1) the <a href="/Structure/cdd/wrpsb.cgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">CD-Search</a>, which uses a <a href="/books/n/handbook/A1237/#app9">BLAST</a>-based algorithm to search the position-specific scoring matrices (<a href="/books/n/handbook/A1237/#app149">PSSM</a>) of CDD alignments; (2) the CD-Browser, which provides a graphic display of domains of interest, along with the sequence alignment; and (3) the Conserved Domain Architecture Retrieval Tool (<a href="/Structure/lexington/lexington.cgi?cmd=rps" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">CDART</a>), which searches for proteins with similar domain architectures.</p><p>All the above databases and tools are discussed in more detail in other parts of this Chapter, including tips on how to make the best use of them.</p></div><div id="A97"><h2 id="_A97_">Content of the Molecular Modeling Database (MMDB)</h2><div id="A98"><h3>Sources of Primary Data</h3><p>To <a class="def" href="/books/n/handbook/A1237/def-item/app209/">build</a> <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> (<a class="bk_pop" href="#A236">1</a>), 3D structure data are retrieved from the <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> database (<a class="bk_pop" href="#A241">6</a>) administered by the Research Collaboratory for Structural Bioinformatics (<a href="/books/n/handbook/A1237/#app154">RCSB</a>). In all cases, the structures in MMDB have been determined by experimental methods, primarily X-ray crystallography and Nuclear Magnetic Resonance (<a href="/books/n/handbook/A1237/#app122">NMR</a>) spectroscopy. Theoretical structure models are omitted. The data in each record are then checked for agreement between the atomic coordinates and the primary sequence, and the sequence data are then extracted from the coordinate set. The resulting agreement between sequence and structure allows the record to be linked efficiently into searches and alignment displays involving other <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> databases.</p><p>The data are converted into <a href="/books/n/handbook/A1237/#app5">ASN</a>.1 (<a class="bk_pop" href="#A242">7</a>), which can be parsed easily and can also accept numerous annotations to the structure data. In contrast to a <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> record, a <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> record in <a class="def" href="/books/n/handbook/A1237/def-item/app5/">ASN.1</a> contains all necessary bonding information in addition to sequence information, allowing consistent display of the 3D structure using <a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a>. The annotations provided in the PDB record by the submitting authors are added, along with uniformly defined secondary structure and <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> features. These features support structure-based similarity searches using <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a>. Finally, two coordinate subsets are added to the record: one containing only backbone atoms, and one representing a single-conformer model in cases where multiple conformations or structures were present in the PDB record. Both of these additions further simplify viewing both an individual structure and its alignments with structure neighbors in Cn3D. When this process is complete, the record is assigned a unique <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a>, the <a class="def" href="/books/n/handbook/A1237/def-item/app113/">MMDB-ID</a> (<a href="/books/NBK21095/box/A99/?report=objectonly" target="object" rid-ob="figobA99">Box 1</a>), while also retaining the original four-character PDB code.</p><div class="iconblock whole_rhythm clearfix ten_col boxed-text" id="figA99"><a href="/books/NBK21095/box/A99/?report=objectonly" target="object" title="Box 1" class="img_link icnblk_img" rid-ob="figobA99"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/box-icon.gif" alt="Box Icon" /></a><div class="icnblk_cntnt"><h4 id="A99"><a href="/books/NBK21095/box/A99/?report=objectonly" target="object" rid-ob="figobA99">Box 1</a></h4><p class="float-caption no_bottom_margin">Accession numbers. </p></div></div></div><div id="A103"><h3>Annotation of 3D Domains</h3><p>After initial processing, 3D domains are automatically identified within each <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> record. 3D domains are annotations on individual MMDB structures that define the boundaries of compact substructures contained within them. In this way, they are similar to secondary structure annotations that define the boundaries of helical or β-strand substructures. Because proteins are often similar at the level of domains, <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> compares each 3D <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> to every other one and to complete <a class="def" href="/books/n/handbook/A1237/def-item/app204/">polypeptide</a> chains. The results are stored in <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> as a <b>Related 3D Domain</b> link.</p><p>To identify 3D domains within a <a class="def" href="/books/n/handbook/A1237/def-item/app204/">polypeptide</a> chain, <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a>'s <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> parser searches for one or more breakpoints in the structure. These breakpoints fall between major secondary structure elements such that the ratio of intra- to interdomain contacts remains above a set threshold. The 3D domains identified in this way provide a means to both increase the sensitivity of structure neighbor calculations and also present 3D superpositions based on compact domains as well as on complete polypeptide chains. They are not intended to represent domains identified by comparative sequence and structure analysis, nor do they represent modules that recur in related proteins, although there is often good agreement between domain boundaries identified by these methods.</p></div><div id="A104"><h3>Links to Other NCBI Resources</h3><p>After initially processing the <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> record, structure staff add a number of links and other information that further integrate the <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> record with other <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> resources. To begin, the sequence information extracted from the PDB record is entered into the <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> Protein and/or Nucleotide databases as appropriate, providing a means to retrieve the structure information from sequence searches. As with all sequences in Entrez, precomputed <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> searches are then performed on these sequences, linking them to other molecules of similar sequence. For proteins, these BLAST neighbors may be different than those determined by <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a>; whereas VAST uses a conservative significance threshold, the structural similarities it detects often represent remote relationships not detectable by sequence comparison. The literature citations in the PDB record are linked to <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> so that Entrez searches can allow access to the original descriptions of the structure determinations. Finally, semiautomatic processing of the “source” field of the PDB record provides links to the NCBI Taxonomy database. Although these links normally follow the genus and species information given, in some cases this information is either absent in the PDB record or refers only to how a sample was obtained. In these cases, the staff manually enters the appropriate taxonomy links.</p></div><div id="A105"><h3>The MMDB Record</h3><p>The Structure Summary page for each <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> record summarizes the database content for that record and serves as a starting point for analyzing the record using the <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> structure tools (<a class="figpopup" href="/books/NBK21095/figure/A106/?report=objectonly" target="object" rid-figpopup="figA106" rid-ob="figobA106">Figure 2</a>).
|
||
</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA106" co-legend-rid="figlgndA106"><a href="/books/NBK21095/figure/A106/?report=objectonly" target="object" title="Figure 2" class="img_link icnblk_img figpopup" rid-figpopup="figA106" rid-ob="figobA106"><img class="small-thumb" src="/books/NBK21095/bin/ch3f2.gif" src-large="/books/NBK21095/bin/ch3f2.jpg" alt="Figure 2. The Structure Summary page." /></a><div class="icnblk_cntnt" id="figlgndA106"><h4 id="A106"><a href="/books/NBK21095/figure/A106/?report=objectonly" target="object" rid-ob="figobA106">Figure 2</a></h4><p class="float-caption no_bottom_margin">The Structure Summary page. The page consists of three parts: the header, the view bar, and the graphic display. The header contains basic identifying information about the record: a description of the protein (<i>Description:</i>), the author list (<i>Deposition:</i> <a href="/books/NBK21095/figure/A106/?report=objectonly" target="object" rid-ob="figobA106">(more...)</a></p></div></div></div><div id="A107"><h3>VAST Structure Neighbors</h3><p>Although <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> itself is not a database, the VAST results computed for each <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> record are stored with this record and are summarized on a separate page for the whole <a class="def" href="/books/n/handbook/A1237/def-item/app204/">polypeptide</a> chain as well as for each 3D <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> found in the protein (<a class="figpopup" href="/books/NBK21095/figure/A108/?report=objectonly" target="object" rid-figpopup="figA108" rid-ob="figobA108">Figure 3</a>). These pages can be accessed most easily by clicking on either the chain bar or the 3D Domain bar in the graphic display of the Structure Summary page (<a class="figpopup" href="/books/NBK21095/figure/A106/?report=objectonly" target="object" rid-figpopup="figA106" rid-ob="figobA106">Figure 2</a>).
|
||
</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA108" co-legend-rid="figlgndA108"><a href="/books/NBK21095/figure/A108/?report=objectonly" target="object" title="Figure 3" class="img_link icnblk_img figpopup" rid-figpopup="figA108" rid-ob="figobA108"><img class="small-thumb" src="/books/NBK21095/bin/ch3f3.gif" src-large="/books/NBK21095/bin/ch3f3.jpg" alt="Figure 3. VAST Structure Neighbors page." /></a><div class="icnblk_cntnt" id="figlgndA108"><h4 id="A108"><a href="/books/NBK21095/figure/A108/?report=objectonly" target="object" rid-ob="figobA108">Figure 3</a></h4><p class="float-caption no_bottom_margin">VAST Structure Neighbors page. The <i>top portion</i> of the page contains identifying information about the 3D Domain, along with three functional bars. (<i>a</i>) The View bar. This bar allows a user to view a selected alignment either as a graphic using Cn3D or <a href="/books/NBK21095/figure/A108/?report=objectonly" target="object" rid-ob="figobA108">(more...)</a></p></div></div></div><div id="A109"><h3>nr-PDB</h3><p>The non-redundant <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> database (<a class="def" href="/books/n/handbook/A1237/def-item/app123/">nr-PDB</a>) is a collection of four sets of sequence-dissimilar <a class="def" href="/books/n/handbook/A1237/def-item/app26/">cluster</a> PDB <a class="def" href="/books/n/handbook/A1237/def-item/app204/">polypeptide</a> chains assembled by <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> Structure staff. The four sets differ only in their respective levels of non-redundancy. The staff assembles each set by comparing all the chains available from PDB with each other using the <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> algorithm. The chains are then clustered into groups of similar sequence using a single-linkage clustering procedure. Chains within a sequence-similar group are automatically ranked according to the quality of their structural data. Details of the measures used to determine structure precision and completeness and the methodology of assembling the nr-PDB clusters can be found on the nr-PDB <a href="/Structure/VAST/nrpdb.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Web page</a>.</p></div></div><div id="A110"><h2 id="_A110_">Content of the Conserved Domain Database (CDD)</h2><div id="A111"><h3>What Is a Conserved Domain (CD)?</h3><p>CDs are recurring units in <a class="def" href="/books/n/handbook/A1237/def-item/app204/">polypeptide</a> chains (sequence and structure motifs), the extents of which can be determined by comparative analysis. Molecular evolution uses such domains as building blocks and these may be recombined in different arrangements to make different proteins with different functions. The <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> contains sequence alignments that define the features that are conserved within each <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> family. Therefore, the CDD serves as a classification resource that groups proteins based on the presence of these predefined domains. CDD entries often name the domain family and describe the role of conserved residues in binding or catalysis. Conserved domains are displayed in <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> Structure summaries and link to a sequence alignment showing other proteins in which the domain is conserved, which may provide clues on protein function.</p></div><div id="A112"><h3>Sources of Primary Data</h3><p>The collections of <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> alignments in the <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> are imported either from two databases outside of the <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a>, named <a class="def" href="/books/n/handbook/A1237/def-item/app131/">Pfam</a> (<a class="bk_pop" href="#A243">8</a>) and <a class="def" href="/books/n/handbook/A1237/def-item/app166/">SMART</a> (<a class="bk_pop" href="#A244">9</a>); from the NCBI COB database; from another NCBI collection named LOAD; and from a database curated by the CDD staff. The first task is to identify the underlying sequences in each collection and then link these sequences to the corresponding ones in <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a>. If the CDD staff cannot find the Accession numbers for the sequences in the records from the source databases, they locate appropriate sequences using <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a>. Particular attention is paid to any resulting match that is linked to a structure record in <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a>, and the staff substitute alignment rows with such sequences whenever possible. After the staff imports a collection, they then choose a sequence that best represents the family. Whenever possible, the staff chooses a representative that has a structure record in MMDB.</p></div><div id="A113"><h3>The Position-specific Score Matrix (PSSM)</h3><p>Once imported and constructed, each <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> alignment in <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> is used to calculate a model sequence, called a <a href="/books/n/handbook/A1237/#app29">consensus sequence</a>, for each <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a>. The <a class="def" href="/books/n/handbook/A1237/def-item/app29/">consensus sequence</a> lists the most frequently found residue in each position in the alignment; however, for a sequence position to be included in the consensus sequence, it must be present in at least 50% of the aligned sequences. Aligned columns covered by the consensus sequence are then used to calculate a <a href="/books/n/handbook/A1237/#app149">PSSM</a>, which memorizes the degree to which particular residues are conserved at each position in the sequence. Once calculated, the <a class="def" href="/books/n/handbook/A1237/def-item/app149/">PSSM</a> is stored with the alignment and becomes part of the CDD. The <a href="/books/n/handbook/A1237/#app159">RPS-BLAST</a> tool locates CDs within a query sequence by searching against this database of PSSMs.</p></div><div id="A114"><h3>Reverse Position-specific BLAST (RPS-BLAST)</h3><p><a class="def" href="/books/n/handbook/A1237/def-item/app159/">RPS-BLAST</a> (<a href="/books/n/handbook/ch16/">Chapter 16</a>) is a variant of the popular Position-specific Iterated BLAST (<a class="def" href="/books/n/handbook/A1237/def-item/app148/">PSI-BLAST</a>) program. PSI-BLAST finds sequences similar to the query and uses the resulting alignments to <a class="def" href="/books/n/handbook/A1237/def-item/app209/">build</a> a <a class="def" href="/books/n/handbook/A1237/def-item/app149/">PSSM</a> for the query. With this PSSM the database is scanned again to draw in more hits and further refine the scoring model. RPS-BLAST uses a query sequence to search a database of precalculated PSSMs and report significant hits in a single pass. The role of the PSSM has changed from “query” to “subject”; hence, the term “reverse” in RPS-BLAST. RPS-BLAST is the search tool used in the <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a>-Search service.</p></div><div id="A115"><h3>The CD Summary</h3><p>Analogous to the Structure Summary page, the <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> Summary page displays the available information about a given CD and offers various links for either viewing the CD alignment or initiating further searches (<a class="figpopup" href="/books/NBK21095/figure/A116/?report=objectonly" target="object" rid-figpopup="figA116" rid-ob="figobA116">Figure 4</a>). The CD Summary page can be retrieved by selecting the CD name on any page.
|
||
</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA116" co-legend-rid="figlgndA116"><a href="/books/NBK21095/figure/A116/?report=objectonly" target="object" title="Figure 4" class="img_link icnblk_img figpopup" rid-figpopup="figA116" rid-ob="figobA116"><img class="small-thumb" src="/books/NBK21095/bin/ch3f4.gif" src-large="/books/NBK21095/bin/ch3f4.jpg" alt="Figure 4. CD summary page." /></a><div class="icnblk_cntnt" id="figlgndA116"><h4 id="A116"><a href="/books/NBK21095/figure/A116/?report=objectonly" target="object" rid-ob="figobA116">Figure 4</a></h4><p class="float-caption no_bottom_margin">CD summary page. The <i>top</i> of the page serves as a header and reports a variety of identifying information, including the name and description of the CD, other related CDs with links to their summary pages, as well as the source database, status, and creation <a href="/books/NBK21095/figure/A116/?report=objectonly" target="object" rid-ob="figobA116">(more...)</a></p></div></div></div><div id="A1760"><h3>CD Records Curated at NCBI</h3><p>In 2002, <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> released the first group of curated <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> records, a new and expanding set of annotated protein multiple sequence alignments and corresponding structure alignments. These new records have Accession numbers beginning with “cd” and have been added to the default CD-Search database. Most curated CD records are based on existing family descriptions from <a class="def" href="/books/n/handbook/A1237/def-item/app166/">SMART</a> and <a class="def" href="/books/n/handbook/A1237/def-item/app131/">Pfam</a>, but the alignments may have been revised extensively by quantitatively using three-dimensional structures and by re-examining the <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> extent. In addition, <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> curators annotate conserved functional residues, ligands, and co-factors contained within the structures. They also record evidence for these sites as pointers to relevant literature or to three-dimensional structures exemplifying their properties. These annotations may be viewed using <a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a> and thus provide a direct way of visualizing functional properties of a protein domain in the context of its three-dimensional structure. (See <a href="/books/NBK21095/box/A179/?report=objectonly" target="object" rid-ob="figobA179">Box 3</a> and <a class="figpopup" href="/books/NBK21095/figure/A184/?report=objectonly" target="object" rid-figpopup="figA184" rid-ob="figobA184">Figure 7</a>.)</p><div class="iconblock whole_rhythm clearfix ten_col boxed-text" id="figA179"><a href="/books/NBK21095/box/A179/?report=objectonly" target="object" title="Box 3" class="img_link icnblk_img" rid-ob="figobA179"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/box-icon.gif" alt="Box Icon" /></a><div class="icnblk_cntnt"><h4 id="A179"><a href="/books/NBK21095/box/A179/?report=objectonly" target="object" rid-ob="figobA179">Box 3</a></h4><p class="float-caption no_bottom_margin">Example query: finding and viewing CDs in a protein. </p></div></div><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA184" co-legend-rid="figlgndA184"><a href="/books/NBK21095/figure/A184/?report=objectonly" target="object" title="Figure 7" class="img_link icnblk_img figpopup" rid-figpopup="figA184" rid-ob="figobA184"><img class="small-thumb" src="/books/NBK21095/bin/ch3f7.gif" src-large="/books/NBK21095/bin/ch3f7.jpg" alt="Figure 7. Sequence and structure views of the TOP1Ac conserved domain common to type III bacterial and eukaryotic DNA topoisomerases." /></a><div class="icnblk_cntnt" id="figlgndA184"><h4 id="A184"><a href="/books/NBK21095/figure/A184/?report=objectonly" target="object" rid-ob="figobA184">Figure 7</a></h4><p class="float-caption no_bottom_margin">Sequence and structure views of the TOP1Ac conserved domain common to type III bacterial and eukaryotic DNA topoisomerases. The <i>upper window</i> displays the structure of the domain with the residues colored according to their sequence conservation, with <a href="/books/NBK21095/figure/A184/?report=objectonly" target="object" rid-ob="figobA184">(more...)</a></p></div></div></div><div id="A117"><h3>The Distinction between 3D Domains and CDs</h3><p>The term “<a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a>” refers in general to a distinct functional and/or structural unit of a protein. Each <a class="def" href="/books/n/handbook/A1237/def-item/app204/">polypeptide</a> chain in <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> is analyzed for the presence of two classes of domains, and it is important for users to understand the difference between them. One class, called 3D Domains, is based solely on similar, compact substructures, whereas the second class, called Conserved Domains (CDs), is based solely on conserved sequence motifs. These two classifications often agree, because the compact substructures within a protein often correspond to domains joined by recombination in the evolutionary history of a protein. Note that <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> links can be identified even when no 3D structures within a family are known. Moreover, 3D Domain links may also indicate relationships either to structures not included in <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> entries or to structures so distantly related that no significant similarity can be found by sequence comparisons.</p></div></div><div id="A118"><h2 id="_A118_">Finding and Viewing Structures</h2><p>For an example query on finding and viewing structures, see <a href="/books/NBK21095/box/A119/?report=objectonly" target="object" rid-ob="figobA119">Box 2</a>.</p><div class="iconblock whole_rhythm clearfix ten_col boxed-text" id="figA119"><a href="/books/NBK21095/box/A119/?report=objectonly" target="object" title="Box 2" class="img_link icnblk_img" rid-ob="figobA119"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/box-icon.gif" alt="Box Icon" /></a><div class="icnblk_cntnt"><h4 id="A119"><a href="/books/NBK21095/box/A119/?report=objectonly" target="object" rid-ob="figobA119">Box 2</a></h4><p class="float-caption no_bottom_margin">Example query: finding and viewing structural data of a protein. </p></div></div><p>
|
||
|
||
</p><div id="A127"><h3>Why Would I Want to Do This?</h3>
|
||
<ul><li id="A128" class="half_rhythm"><div> To determine the overall shape and size of a protein</div></li><li id="A129" class="half_rhythm"><div> To locate a residue of interest in the overall structure</div></li><li id="A130" class="half_rhythm"><div> To locate residues in close proximity to a residue of interest</div></li><li id="A131" class="half_rhythm"><div> To develop or test chemical hypotheses regarding an enzyme mechanism</div></li><li id="A132" class="half_rhythm"><div> To locate or predict possible binding sites of a ligand</div></li><li id="A133" class="half_rhythm"><div> To interpret <a class="def" href="/books/n/handbook/A1237/def-item/app115/">mutation</a> studies</div></li><li id="A134" class="half_rhythm"><div> To find areas of positive or negative charge on the protein surface</div></li><li id="A135" class="half_rhythm"><div> To locate particularly hydrophobic or hydrophilic regions of a protein</div></li><li id="A136" class="half_rhythm"><div> To infer the 3D structure and related properties of a protein with unknown structure from the structure of a <a href="/books/n/handbook/A1237/#app73">homologous</a> protein</div></li><li id="A137" class="half_rhythm"><div> To study evolutionary processes at the level of molecular structure</div></li><li id="A138" class="half_rhythm"><div> To study the function of a protein</div></li><li id="A139" class="half_rhythm"><div> To study the molecular basis of disease and design novel treatments</div></li></ul>
|
||
<div id="A140"><h4>How to Begin</h4><p>The first step to any structural analysis at <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> is to find the structure records for the protein of interest or for proteins similar to it. One may search <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> directly by entering search terms such as <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> code, protein name, author, or journal in the <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> Structure <b>Search</b> box on the Structure <a href="/Structure" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">homepage</a>. Alternative points of entry are shown below.</p><p>By using the full array of <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> search tools, the resulting list of <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> records can be honed, ideally, to a workable list from which a record can be selected. Users should note that multiple records may exist for a given protein, reflecting different experimental techniques, conditions, and the presence or absence of various ligands or metal ions. Records may also contain different fragments of the full-length molecule. In addition, many structures of mutant proteins are also available. The <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> record for a given structure generally contains some description of the experimental conditions under which the structure was determined, and this file can be accessed by selecting the PDB code link at the top of the Structure Summary page.</p></div></div><div id="A141"><h3>Alternative Points of Entry</h3><p>Structure Summary pages can also be found from the following <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> databases and tools:</p>
|
||
<ul><li id="A142" class="half_rhythm"><div> Select the Structure <b>links</b> to the right of any <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> record found; records with Structure links can also be located by choosing <b>Structure links</b> from the <b>Display</b> pull-down menu.</div></li><li id="A143" class="half_rhythm"><div> Select the <b>Related Sequences</b> link to the right of an <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> record to find proteins related by sequence similarity and then select <b>Structure links</b> in the <b>Display</b> pull-down menu.</div></li><li id="A144" class="half_rhythm"><div> Choose the <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> database from a <a href="/books/n/handbook/A1237/#app11">blastp</a> (protein-protein <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a>) search; only sequences with structure records will be retrieved by BLAST. The <b>Related Structures</b> link provides 3D views in <a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a>.</div></li><li id="A145" class="half_rhythm"><div> Select the <b>3D Structures</b> button on any <a href="/books/n/handbook/A1237/#app13">BLink</a> report to show those <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> hits for which structural data are available.</div></li><li id="A1761" class="half_rhythm"><div>From the results of any protein <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> search, click on a red 'S' linkout to view the sequence alignment with a structure record.</div></li></ul>
|
||
</div><div id="A146"><h3>Viewing 3D Structures</h3><div id="A147"><h4>3D Domains</h4><p>The 3D domains of a protein are displayed on the Structure Summary page. It is useful to know how many 3D domains a protein contains and whether they are continuous in sequence when viewing the full 3D structure of the molecule.</p></div><div id="A148"><h4>Secondary Structure</h4><p>Knowing the secondary structure of a protein can also be a useful prelude to viewing the 3D structure of the molecule. The secondary structure can be viewed easily by first selecting the <b>Protein</b> link to the left of the desired chain in the graphic display. Finding oneself in <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> Protein, selecting <b>Graphics</b> in the Display pull-down menu presents secondary structure diagrams for the molecule.</p></div><div id="A149"><h4>Full Protein Structures</h4><p><a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a> is a software package for displaying 3D structures of proteins. Once it has been <a href="/Structure/CN3D/cn3dinstall.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">installed</a> and the Internet browser has been configured correctly, simply selecting the <b>View 3D Structure</b> button on a Structure Summary page launches the application. Once the structure is loaded, a user can manipulate and annotate it using an array of options as described in the <a href="/Structure/CN3D/cn3dtut.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Cn3D Tutorial</a>. By default, Cn3D colors the structure according to the secondary structure elements. However, another useful view is to color the protein by <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> (see <b>Style</b> menu options), using the same color scheme as is shown in the graphic display on the Structure Summary page. These color changes also affect the residues displayed in the Sequence/Alignment Viewer, allowing the identification of domain or secondary structure elements in the primary sequence. In addition to Cn3D, users can also display 3D structures with RasMol or Mage. Structures can also be saved locally as an <a class="def" href="/books/n/handbook/A1237/def-item/app5/">ASN.1</a>, <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a>, or Mage file (depending on the choice of structure viewer) for later display.</p></div></div></div><div id="A150"><h2 id="_A150_">Finding and Viewing Structure Neighbors</h2><p>For an example query on finding and viewing structure neighbors, see <a href="/books/NBK21095/box/A119/?report=objectonly" target="object" rid-ob="figobA119">Box 2</a>.</p><div id="A151"><h3>Why Would I Want to Do This?</h3>
|
||
<ul><li id="A152" class="half_rhythm"><div> To determine structurally conserved regions in a protein family</div></li><li id="A153" class="half_rhythm"><div> To locate the structural equivalent of a residue of interest in another related protein</div></li><li id="A154" class="half_rhythm"><div> To gain insights into the allowable structural variability in a particular protein family</div></li><li id="A155" class="half_rhythm"><div> To develop or test chemical hypotheses regarding an enzyme mechanism</div></li><li id="A156" class="half_rhythm"><div> To predict possible binding sites of a ligand from the location of a binding site in a related protein</div></li><li id="A157" class="half_rhythm"><div> To identify sites where conformational changes are concentrated</div></li><li id="A158" class="half_rhythm"><div> To interpret <a class="def" href="/books/n/handbook/A1237/def-item/app115/">mutation</a> studies</div></li><li id="A159" class="half_rhythm"><div> To find areas of conserved positive or negative charge on the protein surface</div></li><li id="A160" class="half_rhythm"><div> To locate conserved hydrophobic or hydrophilic regions of a protein</div></li><li id="A161" class="half_rhythm"><div> To identify evolutionary relationships across protein families</div></li><li id="A162" class="half_rhythm"><div> To identify functionally equivalent proteins with little or no sequence conservation</div></li></ul>
|
||
</div><div id="A163"><h3>How to Begin</h3><p>The Vector Alignment Search Tool (<a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a>) is used to calculate similar structures on each protein contained in the <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a>. The graphic display on each Structure Summary page (<a class="figpopup" href="/books/NBK21095/figure/A106/?report=objectonly" target="object" rid-figpopup="figA106" rid-ob="figobA106">Figure 2</a>) links directly to the relevant VAST results for both whole proteins and 3D domains:</p>
|
||
<ul><li id="A164" class="half_rhythm"><div> The 3D Domains link transfers the user to <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> 3D Domains, showing a list of the <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> neighbors.</div></li><li id="A165" class="half_rhythm"><div> Selecting the chain bar displays the <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> Structure Neighbors page for the entire chain.</div></li><li id="A166" class="half_rhythm"><div> Selecting a 3D Domain bar displays the <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> Structure Neighbors page for the selected <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a>.</div></li></ul>
|
||
</div><div id="A167"><h3>Alternative Points of Entry</h3>
|
||
<ul><li id="A169" class="half_rhythm"><div> From any <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> search, select <b>Related 3D Domains</b> to the right of any record found to view the Vast Structure Neighbors page.</div></li></ul>
|
||
<div id="A170"><h4>Viewing a 2D Alignment of Structure Neighbors</h4><p>A graphic 2D <a class="def" href="/books/n/handbook/A1237/def-item/app75/">HTML</a> alignment of <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> neighbors can be viewed as follows:</p>
|
||
<ul><li id="A171" class="half_rhythm"><div> On the lower portion of the <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> Structure Neighbors page (<a class="figpopup" href="/books/NBK21095/figure/A108/?report=objectonly" target="object" rid-figpopup="figA108" rid-ob="figobA108">Figure 3</a>), select the desired neighbors to view by checking the boxes to their left.</div></li><li id="A172" class="half_rhythm"><div> On the <b>View/Save</b> bar, configure the pull-down menus to the right of the <b>View Alignment</b> button.</div></li><li id="A173" class="half_rhythm"><div> Select <b>View Alignment</b>.</div></li></ul>
|
||
</div><div id="A174"><h4>Viewing a 3D Alignment of Structure Neighbors</h4><p>Alignments of <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> structure neighbors can be viewed as a 3D image using <a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a>.</p>
|
||
<ul><li id="A175" class="half_rhythm"><div> On the lower portion of the <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> Structure Neighbors page (<a class="figpopup" href="/books/NBK21095/figure/A108/?report=objectonly" target="object" rid-figpopup="figA108" rid-ob="figobA108">Figure 3</a>), select the desired neighbors to view by checking the boxes to their left.</div></li><li id="A176" class="half_rhythm"><div> On the <b>View/Save</b> bar, configure the pull-down menus to the right of the <b>View 3D Structure</b> button.
|
||
</div></li><li id="A177" class="half_rhythm"><div> Select <b>View 3D Structure</b>.</div></li></ul>
|
||
<p><a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a> automatically launches and displays the aligned structures. Each displayed chain has a unique color; however, the portions of the structures involved in the alignment are shown in red. These same colors are also reflected in the Sequence/Alignment Viewer. Among the many viewing options provided by Cn3D, of particular use is the <b>Show/Hide</b> menu that allows only the aligned residues to be viewed, only the aligned domains, or all residues of each chain.</p></div></div></div><div id="A178"><h2 id="_A178_">Finding and Viewing Conserved Domains</h2><p>For an example query on finding and viewing conserved domains, see <a href="/books/NBK21095/box/A179/?report=objectonly" target="object" rid-ob="figobA179">Box 3</a>.</p><p>
|
||
|
||
</p><div id="A185"><h3>Why Would I Want to Do This?</h3>
|
||
<ul><li id="A186" class="half_rhythm"><div> To locate functional domains within a protein</div></li><li id="A187" class="half_rhythm"><div> To predict the function of a protein whose function is unknown</div></li><li id="A188" class="half_rhythm"><div> To establish evolutionary relationships across protein families</div></li><li id="A189" class="half_rhythm"><div> To interpret <a class="def" href="/books/n/handbook/A1237/def-item/app115/">mutation</a> studies</div></li><li id="A190" class="half_rhythm"><div> To predict the structure of a protein of unknown structure</div></li></ul>
|
||
</div><div id="A191"><h3>How to Begin</h3><p>Following the Domains link for any protein in <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a>, one can find the conserved domains within that protein. The <a href="/Structure/cdd/wrpsb.cgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">CD-Search</a> (or Protein <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a>, with CD-Search option selected) can be used to find conserved domains (CDs) within a protein. Either the <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a>, gi number, or the <a href="/books/n/handbook/A1237/#app53">FASTA</a> sequence can be used as a query.</p></div><div id="A192"><h3>Alternative Points of Entry</h3><p>Information on the CDs contained within a protein can also be found from these databases and tools:</p>
|
||
<ul><li id="A198" class="half_rhythm"><div> From any <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> search: select the <b>Domains</b> link to the right of a displayed record.</div></li><li id="A193" class="half_rhythm"><div> From the Structure Summary page of a <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> record: this page displays the CDs within each protein chain immediately below the 3D Domain bar in the graphic display. Selecting the <b>CDs</b> link shows the <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a>-Search results page.</div></li><li id="A194" class="half_rhythm"><div> From an <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> Domains search: choose <b>Domains</b> from the Entrez <b>Search</b> pull-down menu and enter a search term to retrieve a list of CDs. Clicking on any resulting <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> displays the CD Summary page. To find the location of this CD in an aligned protein, select the CD link following a protein name in the bottom portion of this page.</div></li><li id="A195" class="half_rhythm"><div> From the <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> page: locate CDs by entering text terms into the search box and proceed as for an <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> search.</div></li><li id="A196" class="half_rhythm"><div> From a <a class="def" href="/books/n/handbook/A1237/def-item/app13/">BLink</a> report: select the <b><a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a>-Search</b> button to display the <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a>-Search results page.</div></li><li id="A197" class="half_rhythm"><div> From the <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> main page: follow the <a class="def" href="/books/n/handbook/A1237/def-item/app159/">RPS-BLAST</a> link to load the <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a>-Search page.</div></li></ul>
|
||
</div><div id="A199"><h3>Viewing Conserved Domains</h3><p>Results from a <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> search are displayed as colored bars underneath a sequence ruler. Moving the mouse over these bars reveals the identity of each <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a>; domains are also listed in a format similar to <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> summary output (<a href="/books/n/handbook/ch16/">Chapter 16</a>). Pairwise alignments between the matched region of the target protein and the representative sequence of each domain are shown below the bar. Red letters indicate residues identical to those in the representative sequence, whereas blue letters indicate residues with a positive BLOSUM62 score in the BLAST alignment.</p></div><div id="A200"><h3>Viewing Multiple Alignments of a Query Protein with Members of a Conserved Domain</h3><p>These can be displayed by clicking a <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> bar within a <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> Structure Summary page or from a hyperlinked CD name on a CD-Search results page.</p></div><div id="A201"><h3>Viewing CD Alignments in the Context of 3D Structure</h3><p>If members of a <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> have <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> records, one of these records can be viewed as a 3D image along with the sequence alignment using <a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a> (launched by selecting the pink dot on a CD-Search results page). As in other alignment views, colored capital letters indicate aligned residues, allowing the sequence of the protein sequence of interest to be mapped onto the available 3D structure.</p></div></div><div id="A202"><h2 id="_A202_">Finding and Viewing Proteins with Similar Domain Architectures</h2><p>For an example query on finding and viewing proteins with similar <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> architectures, see <a href="/books/NBK21095/box/A179/?report=objectonly" target="object" rid-ob="figobA179">Box 3</a>.</p><div id="A203"><h3>Why Would I Want to Do This?</h3>
|
||
<ul><li id="A204" class="half_rhythm"><div> To locate related functional domains in other protein families</div></li><li id="A205" class="half_rhythm"><div> To gain insights into how a given <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> is situated within a protein relative to other CDs</div></li><li id="A206" class="half_rhythm"><div> To explore functional links between different CDs</div></li><li id="A207" class="half_rhythm"><div> To predict the function of a protein whose function is unknown</div></li><li id="A208" class="half_rhythm"><div> To establish evolutionary relationships across protein families</div></li></ul>
|
||
</div><div id="A209"><h3>How to Begin</h3><p>Following the <b>Domain Relatives</b> link for any protein in <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a>, one can find other proteins with similar <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> architecture. The Conserved Domain Architecture Retrieval Tool (<a href="/Structure/lexington/lexington.cgi?cmd=rps" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">CDART</a>) can take an <a class="def" href="/books/n/handbook/A1237/def-item/app208/">Accession number</a> or the <a class="def" href="/books/n/handbook/A1237/def-item/app53/">FASTA</a> sequence as a query to find out the domain architecture of a protein sequence and list other proteins with related domain architectures.</p></div><div id="A210"><h3>Alternative Points of Entry</h3>
|
||
<ul><li id="A1762" class="half_rhythm"><div>From a <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a>-Search results page, click <b>Show Domain Relatives</b></div></li><li id="A1763" class="half_rhythm"><div>From a <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a>-Summary page, click the <b>Proteins</b> link</div></li><li id="A1764" class="half_rhythm"><div>From an <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> Domains searc, click the <b>Proteins</b> link in the Links menu</div></li></ul>
|
||
</div><div id="A211"><h3>Results of a CDART Search</h3><p>These are described in <a class="figpopup" href="/books/NBK21095/figure/A212/?report=objectonly" target="object" rid-figpopup="figA212" rid-ob="figobA212">Figure 5</a>. The protein “hits”, which have similar <a class="def" href="/books/n/handbook/A1237/def-item/app38/">domain</a> architectures to the query sequence, can be further refined by taxonomic group, in which the results can be limited to selected nodes of the taxonomic tree. Furthermore, search results may be limited to those that contain only particular conserved domains.
|
||
</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA212" co-legend-rid="figlgndA212"><a href="/books/NBK21095/figure/A212/?report=objectonly" target="object" title="Figure 5" class="img_link icnblk_img figpopup" rid-figpopup="figA212" rid-ob="figobA212"><img class="small-thumb" src="/books/NBK21095/bin/ch3f5.gif" src-large="/books/NBK21095/bin/ch3f5.jpg" alt="Figure 5. A CDART results page." /></a><div class="icnblk_cntnt" id="figlgndA212"><h4 id="A212"><a href="/books/NBK21095/figure/A212/?report=objectonly" target="object" rid-ob="figobA212">Figure 5</a></h4><p class="float-caption no_bottom_margin">A CDART results page. At the <i>top</i> of the CDART results page in a <i>yellow box</i>, the query sequence CDs are represented as “beads on a string”. Each CD had a unique color and shape and is labeled both in the display itself and in a legend located <a href="/books/NBK21095/figure/A212/?report=objectonly" target="object" rid-ob="figobA212">(more...)</a></p></div></div></div></div><div id="A213"><h2 id="_A213_">Links Between Structure and Other Resources</h2><div id="A214"><h3>Integration with Other NCBI Resources</h3><p>As illustrated in the sections above, there are numerous connections between the Structure resources and other databases and tools available at the <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a>. What follows is a listing of major tools that support connections.</p><div id="A215"><h4>Entrez</h4><p>Because <a class="def" href="/books/n/handbook/A1237/def-item/app45/">Entrez</a> is an integrated database system (<a href="/books/n/handbook/ch15/">Chapter 15</a>), the links attached to each structure give immediate access to <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>, Protein, Nucleotide, 3D Domain, <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a>, or Taxonomy records.</p></div><div id="A216"><h4>BLAST</h4><p>Although the <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> service is designed to find matches based solely on sequence, the sequences of Structure records are included in the BLAST databases, and by selecting the <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> search database, BLAST searches only the protein sequences provided by <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> records. A new <b>Related Structure</b> link provides 3D views for sequences with structure data identified in a BLAST search.</p></div><div id="A217"><h4>BLink</h4><p>The <a class="def" href="/books/n/handbook/A1237/def-item/app13/">BLink</a> report represents a precomputed list of similar proteins for many proteins (see, for example, links from <a class="def" href="/books/n/handbook/A1237/def-item/app97/">Entrez Gene</a> records; <a href="/books/n/handbook/ch19/">Chapter 19</a>). The <b>3D Structures</b> option on any BLink report shows the <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> hits that have 3D structure data in <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a>, whereas the <b><a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a>-Search</b> button displays the <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a>-Search results page for the query protein.</p></div><div id="A218"><h4>Microbial Genomes</h4><p>A particularly useful interface with the structural databases is provided on the <a href="/PMGifs/Genomes/micr.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Microbial Genomes page</a> (<a class="bk_pop" href="#A245">10</a>). To the left of the list of genomes are several hyperlinks, two of which offer users direct access to structural information. The red <b>[D]</b> link displays a listing of every protein in the genome, each with a link to a <a class="def" href="/books/n/handbook/A1237/def-item/app13/">BLink</a> page showing the results of a <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> pdb search for that protein. The <b>[S]</b> link displays a similar protein list for the selected genome, but now with a listing of the conserved domains found in each protein by a <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a>-Search.</p></div></div><div id="A219"><h3>Links to Non-NCBI Resources</h3><div id="A220"><h4>The Protein Data Bank (PDB)</h4><p>As stated elsewhere, all records in the <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> are obtained originally from the Protein Data Bank (<a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a>) (<a class="bk_pop" href="#A241">6</a>). Links to the original PDB records are located on the Structure Summary page of each MMDB record. Updates of the MMDB with new PDB records occur once a month.</p></div><div id="A221"><h4>Pfam and SMART</h4><p>The <a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> staff imports <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> collections from both the <a class="def" href="/books/n/handbook/A1237/def-item/app131/">Pfam</a> and <a class="def" href="/books/n/handbook/A1237/def-item/app166/">SMART</a> databases. Links to the original records in these databases are located on the appropriate CD Summary page. Both Pfam and SMART are updated several times per year in roughly bimonthly intervals, and the CDD staff update CDD accordingly.</p></div></div></div><div id="A222"><h2 id="_A222_">Saving Output from Database Searches</h2><div id="A223"><h3>Exporting Graphics Files from Cn3D</h3><p>Structures displayed in <a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a> can be exported as a Portable Network Graphics (<a href="/books/n/handbook/A1237/#app140">PNG</a>) file from within Cn3D (the Export <a class="def" href="/books/n/handbook/A1237/def-item/app140/">PNG</a> command in the <b>File</b> menu). The structure file itself, in the orientation currently being viewed, can also be saved for later launching in Cn3D.</p></div><div id="A224"><h3>Saving Individual MMDB Records</h3><p>Individual <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> records can be saved/downloaded to a local computer directly from the Structure Summary page for that record. <b>Save File</b> in the <b>View</b> bar downloads the file in a choice of three formats: <a class="def" href="/books/n/handbook/A1237/def-item/app5/">ASN.1</a> (select <b><a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a></b>); <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> (select <b>RasMol</b>); or Mage (select <b>Mage</b>).</p></div><div id="A225"><h3>Saving VAST Alignments</h3><p>Alignments of <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> neighbors can be saved/downloaded from the VAST Structure Neighbors page of any <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> record. By selecting options in the <b>View Alignment</b> pull-down menu, the alignment data can be saved, formatted as <a class="def" href="/books/n/handbook/A1237/def-item/app75/">HTML</a>, text, or <a href="/books/n/handbook/A1237/#app106">mFASTA</a>, and then saved.</p></div></div><div id="A226"><h2 id="_A226_">FTP</h2><div id="A1765"><h3>MMDB</h3><p>Users can download the <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> Structure databases from the NCBI <a class="def" href="/books/n/handbook/A1237/def-item/app58/">FTP</a> site: <a href="ftp://ftp.ncbi.nih.gov/mmdb" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">ftp://ftp.ncbi.nih.gov/mmdb</a>. A Readme file contains descriptions of the contents and information about recent updates. Within the mmdb directory are four subdirectories that contain the following data:</p>
|
||
<ul><li id="A227" class="half_rhythm"><div> mmdbdata: the current <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> database (NOTE: these files can not be read directly by <a class="def" href="/books/n/handbook/A1237/def-item/app27/">Cn3D</a>).</div></li><li id="A228" class="half_rhythm"><div> vastdata: the current set of <a class="def" href="/books/n/handbook/A1237/def-item/app193/">VAST</a> neighbor annotations to <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> records</div></li><li id="A229" class="half_rhythm"><div> nrtable: the current non-redundant <a class="def" href="/books/n/handbook/A1237/def-item/app130/">PDB</a> database</div></li><li id="A230" class="half_rhythm"><div> pdbeast: table listing the taxonomic classification of <a class="def" href="/books/n/handbook/A1237/def-item/app112/">MMDB</a> records</div></li></ul>
|
||
</div><div id="A1766"><h3>CDD</h3><p><a class="def" href="/books/n/handbook/A1237/def-item/app20/">CDD</a> data can be downloaded from <a href="ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd</a>. A Readme file contains descriptions of the data archives. Users can download the PSSMs for each <a class="def" href="/books/n/handbook/A1237/def-item/app18/">CD</a> record, the sequence alignments in <a class="def" href="/books/n/handbook/A1237/def-item/app106/">mFASTA</a> format, or a text file containing the accessions and descriptions of all CD records. </p></div></div><div id="A231"><h2 id="_A231_">Frequently Asked Questions</h2>
|
||
<ul><li id="A232" class="half_rhythm"><div>
|
||
<a href="http://www.ncbi.nih.gov/Structure/CN3D/cn3dfaq.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Cn3D</a>
|
||
</div></li><li id="A233" class="half_rhythm"><div>
|
||
<a href="http://www.ncbi.nih.gov/Structure/VAST/vastsearch_faq.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">VAST searches</a>
|
||
</div></li><li id="A234" class="half_rhythm"><div>
|
||
<a href="/Structure/cdd/cdd_help.shtml" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">CDD</a>
|
||
</div></li></ul>
|
||
</div><div id="A235"><h2 id="_A235_">References</h2><dl class="temp-labeled-list"><dt>1.</dt><dd><div class="bk_ref" id="A236">Wang Y , Anderson JB , Chen J , Geer LY , He S , Hurwitz DI , Liebert CA , Madej T , Marchler GH , Marchler-Bauer A , Panchenko AR , Shoemaker BA , Song JS , Thiessen PA , Yamashita RA , Bryant SH . MMDB: Entrez's 3D-structure database. <span><span class="ref-journal">Nucleic Acids Res. </span>2002;<span class="ref-vol">30</span>:249–252.</span> [<a href="/pmc/articles/PMC99072/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC99072</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/11752307" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11752307</span></a>]</div></dd><dt>2.</dt><dd><div class="bk_ref" id="A237">Wang Y , Geer LY , Chappey C , Kans JA , Bryant SH . Cn3D: sequence and structure views for Entrez. <span><span class="ref-journal">Trends Biochem Sci. </span>2000;<span class="ref-vol">25</span>:300–302.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/10838572" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 10838572</span></a>]</div></dd><dt>3.</dt><dd><div class="bk_ref" id="A238">Madej T , Gibrat J-F , Bryant SH . Threading a database of protein cores. <span><span class="ref-journal">Proteins. </span>1995;<span class="ref-vol">23</span>:356–369.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/8710828" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 8710828</span></a>]</div></dd><dt>4.</dt><dd><div class="bk_ref" id="A239">Gibrat J-F , Madej T , Bryant SH . Surprising similarities in structure comparison. <span><span class="ref-journal">Curr Opin Struct Biol. </span>1996;<span class="ref-vol">6</span>:377–385.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/8804824" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 8804824</span></a>]</div></dd><dt>5.</dt><dd><div class="bk_ref" id="A240">Marchler-Bauer A , Panchenko AR , Shoemaker BA , Thiessen PA , Geer LY , Bryant SH . CDD: a database of conserved domain alignments with links to domain three-dimensional structure. <span><span class="ref-journal">Nucleic Acids Res. </span>2002;<span class="ref-vol">30</span>:281–283.</span> [<a href="/pmc/articles/PMC99109/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC99109</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/11752315" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11752315</span></a>]</div></dd><dt>6.</dt><dd><div class="bk_ref" id="A241">Westbrook J , Feng Z , Jain S , Bhat TN , Thanki N , Ravichandran V , Gilliland GL , Bluhm W , Weissig H , Greer DS , Bourne PE , Berman HM . The Protein Data Bank: unifying the archive. <span><span class="ref-journal">Nucleic Acids Res. </span>2002;<span class="ref-vol">30</span>:245–248.</span> [<a href="/pmc/articles/PMC99110/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC99110</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/11752306" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11752306</span></a>]</div></dd><dt>7.</dt><dd><div class="bk_ref" id="A242">Ohkawa H , Ostell J , Bryant S . MMDB: an ASN.1 specification for macromolecular structure. <span><span class="ref-journal">Proc Int Conf Intell Syst Mol Biol. </span>1995;<span class="ref-vol">3</span>:259–267.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/7584445" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 7584445</span></a>]</div></dd><dt>8.</dt><dd><div class="bk_ref" id="A243">Bateman A , Birney E , Cerruti L , Durbin R , Etwiller L , Eddy SR , Griffiths-Jones S , Howe KL , Marshall M , Sonnhammer ELL . The Pfam proteins family database. <span><span class="ref-journal">Nucleic Acids Res. </span>2002;<span class="ref-vol">30</span>:276–280.</span> [<a href="/pmc/articles/PMC99071/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC99071</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/11752314" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11752314</span></a>]</div></dd><dt>9.</dt><dd><div class="bk_ref" id="A244">Letunic I , Goodstadt L , Dickens NJ , Doerks T , Schultz J , Mott R , Ciccarelli F , Copley RR , Ponting CP , Bork P . SMART: a Web-based tool for the study of genetically mobile domains. Recent improvements to the SMART domain-based sequence annotation resource. <span><span class="ref-journal">Nucleic Acids Res. </span>2002;<span class="ref-vol">30</span>:242–244.</span> [<a href="/pmc/articles/PMC99073/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC99073</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/11752305" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11752305</span></a>]</div></dd><dt>10.</dt><dd><div class="bk_ref" id="A245">Wang Y , Bryant S , Tatusov R , Tatusova T . Links from genome proteins to known 3D structures. <span><span class="ref-journal">Genome Res. </span>2000;<span class="ref-vol">10</span>:1643–1647.</span> [<a href="/pmc/articles/PMC310938/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC310938</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/11042161" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11042161</span></a>]</div></dd></dl></div><div id="bk_toc_contnr"></div></div></div>
|
||
<div class="post-content"><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div><div class="small"><span class="label">Bookshelf ID: NBK21095</span></div><div style="margin-top:2em" class="bk_noprnt"><a class="bk_cntns" href="/books/n/handbook/">Contents</a><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/handbook/ch2/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/handbook/ch4/" title="Next page in this title">Next ></a></div></div></div></div>
|
||
|
||
</div>
|
||
|
||
<!-- Custom content below content -->
|
||
<div class="col4">
|
||
|
||
</div>
|
||
|
||
|
||
<!-- Book content -->
|
||
|
||
<!-- Custom contetnt below bottom nav -->
|
||
<div class="col5">
|
||
|
||
</div>
|
||
</div>
|
||
|
||
<div id="rightcolumn" class="four_col col last">
|
||
<!-- Custom content above discovery portlets -->
|
||
<div class="col6">
|
||
<div id="ncbi_share_book"><a href="#" class="ncbi_share" data-ncbi_share_config="popup:false,shorten:true" ref="id=NBK21095&db=books">Share</a></div>
|
||
|
||
</div>
|
||
<div xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>Views</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="PDF_download" id="Shutter"></a></div><div class="portlet_content"><ul xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="simple-list"><li><a href="/books/NBK21095/?report=reader">PubReader</a></li><li><a href="/books/NBK21095/?report=printable">Print View</a></li><li><a data-jig="ncbidialog" href="#_ncbi_dlg_citbx_NBK21095" data-jigconfig="width:400,modal:true">Cite this Page</a><div id="_ncbi_dlg_citbx_NBK21095" style="display:none" title="Cite this Page"><div class="bk_tt">Sayers E, Bryant S. Macromolecular Structure Databases. 2002 Oct 9 [Updated 2003 Aug 13]. In: McEntyre J, Ostell J, editors. The NCBI Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2002-. Chapter 3.<span class="bk_cite_avail"></span></div></div></li><li><a href="/books/NBK21095/pdf/Bookshelf_NBK21095.pdf">PDF version of this page</a> (842K)</li><li><a href="/books/n/handbook/pdf/">PDF version of this title</a> (7.2M)</li><li><a href="#" class="toggle-glossary-link" title="Enable/disable links to the glossary">Disable Glossary Links</a></li></ul></div></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>In this Page</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="page-toc" id="Shutter"></a></div><div class="portlet_content"><ul xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="simple-list"><li><a href="#_abs_rndgid_" ref="log$=inpage&link_id=inpage">Summary</a></li><li><a href="#A95" ref="log$=inpage&link_id=inpage">Overview</a></li><li><a href="#A97" ref="log$=inpage&link_id=inpage">Content of the Molecular Modeling Database (MMDB)</a></li><li><a href="#A110" ref="log$=inpage&link_id=inpage">Content of the Conserved Domain Database (CDD)</a></li><li><a href="#A118" ref="log$=inpage&link_id=inpage">Finding and Viewing Structures</a></li><li><a href="#A150" ref="log$=inpage&link_id=inpage">Finding and Viewing Structure Neighbors</a></li><li><a href="#A178" ref="log$=inpage&link_id=inpage">Finding and Viewing Conserved Domains</a></li><li><a href="#A202" ref="log$=inpage&link_id=inpage">Finding and Viewing Proteins with Similar Domain Architectures</a></li><li><a href="#A213" ref="log$=inpage&link_id=inpage">Links Between Structure and Other Resources</a></li><li><a href="#A222" ref="log$=inpage&link_id=inpage">Saving Output from Database Searches</a></li><li><a href="#A226" ref="log$=inpage&link_id=inpage">FTP</a></li><li><a href="#A231" ref="log$=inpage&link_id=inpage">Frequently Asked Questions</a></li><li><a href="#A235" ref="log$=inpage&link_id=inpage">References</a></li></ul></div></div><div class="portlet"><div class="portlet_head"><div class="portlet_title"><h3><span>Recent Activity</span></h3></div><a name="Shutter" sid="1" href="#" class="portlet_shutter" title="Show/hide content" remembercollapsed="true" pgsec_name="recent_activity" id="Shutter"></a></div><div class="portlet_content"><div xmlns:np="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="HTDisplay" class=""><div class="action"><a href="javascript:historyDisplayState('ClearHT')">Clear</a><a href="javascript:historyDisplayState('HTOff')" class="HTOn">Turn Off</a><a href="javascript:historyDisplayState('HTOn')" class="HTOff">Turn On</a></div><ul id="activity"><li class="ra_rcd ralinkpopper two_line"><a class="htb ralinkpopperctrl" ref="log$=activity&linkpos=1" href="/portal/utils/pageresolver.fcgi?recordid=67da0b6b2f30673f7b090a5a">Macromolecular Structure Databases - The NCBI Handbook</a><div class="ralinkpop offscreen_noflow">Macromolecular Structure Databases - The NCBI Handbook<div class="brieflinkpopdesc"></div></div><div class="tertiary"></div></li><li class="ra_qry two_line"><a class="htb" ref="log$=activity&linkpos=2" href="/portal/utils/pageresolver.fcgi?recordid=67da0b4967c23b31e0bc543d">"Proteins"[jour] <span class="number">(1269)</span></a><div class="tertiary">PMC</div></li><li class="ra_qry two_line"><a class="htb" ref="log$=activity&linkpos=3" href="/portal/utils/pageresolver.fcgi?recordid=67da0b4184f3725e5933b424">"Cell Cycle"[jour] <span class="number">(5560)</span></a><div class="tertiary">PMC</div></li><li class="ra_qry two_line"><a class="htb" ref="log$=activity&linkpos=4" href="/portal/utils/pageresolver.fcgi?recordid=67da0b3c2f30673f7b08830c">"Science"[jour] <span class="number">(5363)</span></a><div class="tertiary">PMC</div></li><li class="ra_qry two_line"><a class="htb" ref="log$=activity&linkpos=5" href="/portal/utils/pageresolver.fcgi?recordid=67da0b37cde49f3df7f56c04">"Biol Direct"[jour] <span class="number">(1009)</span></a><div class="tertiary">PMC</div></li></ul><p class="HTOn">Your browsing activity is empty.</p><p class="HTOff">Activity recording is turned off.</p><p id="turnOn" class="HTOff"><a href="javascript:historyDisplayState('HTOn')">Turn recording back on</a></p><a class="seemore" href="/sites/myncbi/recentactivity">See more...</a></div></div></div>
|
||
|
||
<!-- Custom content below discovery portlets -->
|
||
<div class="col7">
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<!-- Custom content after all -->
|
||
<div class="col8">
|
||
|
||
</div>
|
||
<div class="col9">
|
||
|
||
</div>
|
||
|
||
<script type="text/javascript" src="/corehtml/pmc/js/jquery.scrollTo-1.4.2.js"></script>
|
||
<script type="text/javascript">
|
||
(function($){
|
||
$('.skiplink').each(function(i, item){
|
||
var href = $($(item).attr('href'));
|
||
href.attr('tabindex', '-1').addClass('skiptarget'); // ensure the target can receive focus
|
||
$(item).on('click', function(event){
|
||
event.preventDefault();
|
||
$.scrollTo(href, 0, {
|
||
onAfter: function(){
|
||
href.focus();
|
||
}
|
||
});
|
||
});
|
||
});
|
||
})(jQuery);
|
||
</script>
|
||
</div>
|
||
<div class="bottom">
|
||
|
||
<div id="NCBIFooter_dynamic">
|
||
<!--<component id="Breadcrumbs" label="breadcrumbs"/>
|
||
<component id="Breadcrumbs" label="helpdesk"/>-->
|
||
|
||
</div>
|
||
|
||
<div class="footer" id="footer">
|
||
<section class="icon-section">
|
||
<div id="icon-section-header" class="icon-section_header">Follow NCBI</div>
|
||
<div class="grid-container container">
|
||
<div class="icon-section_container">
|
||
<a class="footer-icon" id="footer_twitter" href="https://twitter.com/ncbi" aria-label="Twitter"><svg xmlns="http://www.w3.org/2000/svg" data-name="Layer 1" viewBox="0 0 300 300">
|
||
<defs>
|
||
<style>
|
||
.cls-11 {
|
||
fill: #737373;
|
||
}
|
||
</style>
|
||
</defs>
|
||
<title>Twitter</title>
|
||
<path class="cls-11" d="M250.11,105.48c-7,3.14-13,3.25-19.27.14,8.12-4.86,8.49-8.27,11.43-17.46a78.8,78.8,0,0,1-25,9.55,39.35,39.35,0,0,0-67,35.85,111.6,111.6,0,0,1-81-41.08A39.37,39.37,0,0,0,81.47,145a39.08,39.08,0,0,1-17.8-4.92c0,.17,0,.33,0,.5a39.32,39.32,0,0,0,31.53,38.54,39.26,39.26,0,0,1-17.75.68,39.37,39.37,0,0,0,36.72,27.3A79.07,79.07,0,0,1,56,223.34,111.31,111.31,0,0,0,116.22,241c72.3,0,111.83-59.9,111.83-111.84,0-1.71,0-3.4-.1-5.09C235.62,118.54,244.84,113.37,250.11,105.48Z">
|
||
</path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_facebook" href="https://www.facebook.com/ncbi.nlm" aria-label="Facebook"><svg xmlns="http://www.w3.org/2000/svg" data-name="Layer 1" viewBox="0 0 300 300">
|
||
<title>Facebook</title>
|
||
<path class="cls-11" d="M210.5,115.12H171.74V97.82c0-8.14,5.39-10,9.19-10h27.14V52l-39.32-.12c-35.66,0-42.42,26.68-42.42,43.77v19.48H99.09v36.32h27.24v109h45.41v-109h35Z">
|
||
</path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_linkedin" href="https://www.linkedin.com/company/ncbinlm" aria-label="LinkedIn"><svg xmlns="http://www.w3.org/2000/svg" data-name="Layer 1" viewBox="0 0 300 300">
|
||
<title>LinkedIn</title>
|
||
<path class="cls-11" d="M101.64,243.37H57.79v-114h43.85Zm-22-131.54h-.26c-13.25,0-21.82-10.36-21.82-21.76,0-11.65,8.84-21.15,22.33-21.15S101.7,78.72,102,90.38C102,101.77,93.4,111.83,79.63,111.83Zm100.93,52.61A17.54,17.54,0,0,0,163,182v61.39H119.18s.51-105.23,0-114H163v13a54.33,54.33,0,0,1,34.54-12.66c26,0,44.39,18.8,44.39,55.29v58.35H198.1V182A17.54,17.54,0,0,0,180.56,164.44Z">
|
||
</path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_github" href="https://github.com/ncbi" aria-label="GitHub"><svg xmlns="http://www.w3.org/2000/svg" data-name="Layer 1" viewBox="0 0 300 300">
|
||
<defs>
|
||
<style>
|
||
.cls-11,
|
||
.cls-12 {
|
||
fill: #737373;
|
||
}
|
||
|
||
.cls-11 {
|
||
fill-rule: evenodd;
|
||
}
|
||
</style>
|
||
</defs>
|
||
<title>GitHub</title>
|
||
<path class="cls-11" d="M151.36,47.28a105.76,105.76,0,0,0-33.43,206.1c5.28,1,7.22-2.3,7.22-5.09,0-2.52-.09-10.85-.14-19.69-29.42,6.4-35.63-12.48-35.63-12.48-4.81-12.22-11.74-15.47-11.74-15.47-9.59-6.56.73-6.43.73-6.43,10.61.75,16.21,10.9,16.21,10.9,9.43,16.17,24.73,11.49,30.77,8.79,1-6.83,3.69-11.5,6.71-14.14C108.57,197.1,83.88,188,83.88,147.51a40.92,40.92,0,0,1,10.9-28.39c-1.1-2.66-4.72-13.42,1-28,0,0,8.88-2.84,29.09,10.84a100.26,100.26,0,0,1,53,0C198,88.3,206.9,91.14,206.9,91.14c5.76,14.56,2.14,25.32,1,28a40.87,40.87,0,0,1,10.89,28.39c0,40.62-24.74,49.56-48.29,52.18,3.79,3.28,7.17,9.71,7.17,19.58,0,14.15-.12,25.54-.12,29,0,2.82,1.9,6.11,7.26,5.07A105.76,105.76,0,0,0,151.36,47.28Z">
|
||
</path>
|
||
<path class="cls-12" d="M85.66,199.12c-.23.52-1.06.68-1.81.32s-1.2-1.06-.95-1.59,1.06-.69,1.82-.33,1.21,1.07.94,1.6Zm-1.3-1">
|
||
</path>
|
||
<path class="cls-12" d="M90,203.89c-.51.47-1.49.25-2.16-.49a1.61,1.61,0,0,1-.31-2.19c.52-.47,1.47-.25,2.17.49s.82,1.72.3,2.19Zm-1-1.08">
|
||
</path>
|
||
<path class="cls-12" d="M94.12,210c-.65.46-1.71,0-2.37-.91s-.64-2.07,0-2.52,1.7,0,2.36.89.65,2.08,0,2.54Zm0,0"></path>
|
||
<path class="cls-12" d="M99.83,215.87c-.58.64-1.82.47-2.72-.41s-1.18-2.06-.6-2.7,1.83-.46,2.74.41,1.2,2.07.58,2.7Zm0,0">
|
||
</path>
|
||
<path class="cls-12" d="M107.71,219.29c-.26.82-1.45,1.2-2.64.85s-2-1.34-1.74-2.17,1.44-1.23,2.65-.85,2,1.32,1.73,2.17Zm0,0">
|
||
</path>
|
||
<path class="cls-12" d="M116.36,219.92c0,.87-1,1.59-2.24,1.61s-2.29-.68-2.3-1.54,1-1.59,2.26-1.61,2.28.67,2.28,1.54Zm0,0">
|
||
</path>
|
||
<path class="cls-12" d="M124.42,218.55c.15.85-.73,1.72-2,1.95s-2.37-.3-2.52-1.14.73-1.75,2-2,2.37.29,2.53,1.16Zm0,0"></path>
|
||
</svg></a>
|
||
<a class="footer-icon" id="footer_blog" href="https://ncbiinsights.ncbi.nlm.nih.gov/" aria-label="Blog">
|
||
<svg xmlns="http://www.w3.org/2000/svg" id="Layer_1" data-name="Layer 1" viewBox="0 0 40 40">
|
||
<defs><style>.cls-1{fill:#737373;}</style></defs>
|
||
<title>NCBI Insights Blog</title>
|
||
<path class="cls-1" d="M14,30a4,4,0,1,1-4-4,4,4,0,0,1,4,4Zm11,3A19,19,0,0,0,7.05,15a1,1,0,0,0-1,1v3a1,1,0,0,0,.93,1A14,14,0,0,1,20,33.07,1,1,0,0,0,21,34h3a1,1,0,0,0,1-1Zm9,0A28,28,0,0,0,7,6,1,1,0,0,0,6,7v3a1,1,0,0,0,1,1A23,23,0,0,1,29,33a1,1,0,0,0,1,1h3A1,1,0,0,0,34,33Z"></path>
|
||
</svg>
|
||
</a>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
|
||
<section class="container-fluid bg-primary">
|
||
<div class="container pt-5">
|
||
<div class="row mt-3">
|
||
<div class="col-lg-3 col-12">
|
||
<p><a class="text-white" href="https://www.nlm.nih.gov/socialmedia/index.html">Connect with NLM</a></p>
|
||
<ul class="list-inline social_media">
|
||
<li class="list-inline-item"><a href="https://twitter.com/NLM_NIH" aria-label="Twitter" target="_blank" rel="noopener noreferrer"><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1" x="0px" y="0px" viewBox="0 0 249 249" style="enable-background:new 0 0 249 249;" xml:space="preserve">
|
||
<style type="text/css">
|
||
.st20 {
|
||
fill: #FFFFFF;
|
||
}
|
||
|
||
.st30 {
|
||
fill: none;
|
||
stroke: #FFFFFF;
|
||
stroke-width: 8;
|
||
stroke-miterlimit: 10;
|
||
}
|
||
</style>
|
||
<title>Twitter</title>
|
||
<g>
|
||
<g>
|
||
<g>
|
||
<path class="st20" d="M192.9,88.1c-5,2.2-9.2,2.3-13.6,0.1c5.7-3.4,6-5.8,8.1-12.3c-5.4,3.2-11.4,5.5-17.6,6.7 c-10.5-11.2-28.1-11.7-39.2-1.2c-7.2,6.8-10.2,16.9-8,26.5c-22.3-1.1-43.1-11.7-57.2-29C58,91.6,61.8,107.9,74,116 c-4.4-0.1-8.7-1.3-12.6-3.4c0,0.1,0,0.2,0,0.4c0,13.2,9.3,24.6,22.3,27.2c-4.1,1.1-8.4,1.3-12.5,0.5c3.6,11.3,14,19,25.9,19.3 c-11.6,9.1-26.4,13.2-41.1,11.5c12.7,8.1,27.4,12.5,42.5,12.5c51,0,78.9-42.2,78.9-78.9c0-1.2,0-2.4-0.1-3.6 C182.7,97.4,189.2,93.7,192.9,88.1z"></path>
|
||
</g>
|
||
</g>
|
||
<circle class="st30" cx="124.4" cy="128.8" r="108.2"></circle>
|
||
</g>
|
||
</svg></a></li>
|
||
<li class="list-inline-item"><a href="https://www.facebook.com/nationallibraryofmedicine" aria-label="Facebook" rel="noopener noreferrer" target="_blank">
|
||
<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1" x="0px" y="0px" viewBox="0 0 249 249" style="enable-background:new 0 0 249 249;" xml:space="preserve">
|
||
<style type="text/css">
|
||
.st10 {
|
||
fill: #FFFFFF;
|
||
}
|
||
|
||
.st110 {
|
||
fill: none;
|
||
stroke: #FFFFFF;
|
||
stroke-width: 8;
|
||
stroke-miterlimit: 10;
|
||
}
|
||
</style>
|
||
<title>Facebook</title>
|
||
<g>
|
||
<g>
|
||
<path class="st10" d="M159,99.1h-24V88.4c0-5,3.3-6.2,5.7-6.2h16.8V60l-24.4-0.1c-22.1,0-26.2,16.5-26.2,27.1v12.1H90v22.5h16.9 v67.5H135v-67.5h21.7L159,99.1z"></path>
|
||
</g>
|
||
</g>
|
||
<circle class="st110" cx="123.6" cy="123.2" r="108.2"></circle>
|
||
</svg>
|
||
</a></li>
|
||
<li class="list-inline-item"><a href="https://www.youtube.com/user/NLMNIH" aria-label="Youtube" target="_blank" rel="noopener noreferrer"><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1" x="0px" y="0px" viewBox="0 0 249 249" style="enable-background:new 0 0 249 249;" xml:space="preserve">
|
||
<title>Youtube</title>
|
||
<style type="text/css">
|
||
.st4 {
|
||
fill: none;
|
||
stroke: #FFFFFF;
|
||
stroke-width: 8;
|
||
stroke-miterlimit: 10;
|
||
}
|
||
|
||
.st5 {
|
||
fill: #FFFFFF;
|
||
}
|
||
</style>
|
||
<circle class="st4" cx="124.2" cy="123.4" r="108.2"></circle>
|
||
<g transform="translate(0,-952.36218)">
|
||
<path class="st5" d="M88.4,1037.4c-10.4,0-18.7,8.3-18.7,18.7v40.1c0,10.4,8.3,18.7,18.7,18.7h72.1c10.4,0,18.7-8.3,18.7-18.7 v-40.1c0-10.4-8.3-18.7-18.7-18.7H88.4z M115.2,1058.8l29.4,17.4l-29.4,17.4V1058.8z"></path>
|
||
</g>
|
||
</svg></a></li>
|
||
</ul>
|
||
</div>
|
||
<div class="col-lg-3 col-12">
|
||
<p class="address_footer text-white">National Library of Medicine<br />
|
||
<a href="https://www.google.com/maps/place/8600+Rockville+Pike,+Bethesda,+MD+20894/@38.9959508,-77.101021,17z/data=!3m1!4b1!4m5!3m4!1s0x89b7c95e25765ddb:0x19156f88b27635b8!8m2!3d38.9959508!4d-77.0988323" class="text-white" target="_blank" rel="noopener noreferrer">8600 Rockville Pike<br />
|
||
Bethesda, MD 20894</a></p>
|
||
</div>
|
||
<div class="col-lg-3 col-12 centered-lg">
|
||
<p><a href="https://www.nlm.nih.gov/web_policies.html" class="text-white">Web Policies</a><br />
|
||
<a href="https://www.nih.gov/institutes-nih/nih-office-director/office-communications-public-liaison/freedom-information-act-office" class="text-white">FOIA</a><br />
|
||
<a href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html" class="text-white" id="vdp">HHS Vulnerability Disclosure</a></p>
|
||
</div>
|
||
<div class="col-lg-3 col-12 centered-lg">
|
||
<p><a class="supportLink text-white" href="https://support.nlm.nih.gov/">Help</a><br />
|
||
<a href="https://www.nlm.nih.gov/accessibility.html" class="text-white">Accessibility</a><br />
|
||
<a href="https://www.nlm.nih.gov/careers/careers.html" class="text-white">Careers</a></p>
|
||
</div>
|
||
</div>
|
||
<div class="row">
|
||
<div class="col-lg-12 centered-lg">
|
||
<nav class="bottom-links">
|
||
<ul class="mt-3">
|
||
<li>
|
||
<a class="text-white" href="//www.nlm.nih.gov/">NLM</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.nih.gov/">NIH</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.hhs.gov/">HHS</a>
|
||
</li>
|
||
<li>
|
||
<a class="text-white" href="https://www.usa.gov/">USA.gov</a>
|
||
</li>
|
||
</ul>
|
||
</nav>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIConfigJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js?v=1"> </script>
|
||
<script type="text/javascript" src="/portal/portal3rc.fcgi/static/js/hfjs2.js"> </script>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<!--/.page-->
|
||
</div>
|
||
<!--/.wrap-->
|
||
</div><!-- /.twelve_col -->
|
||
</div>
|
||
<!-- /.grid -->
|
||
|
||
<span class="PAFAppResources"></span>
|
||
|
||
<!-- BESelector tab -->
|
||
|
||
|
||
|
||
<noscript><img alt="statistics" src="/stat?jsdisabled=true&ncbi_db=books&ncbi_pdid=book-part&ncbi_acc=NBK21095&ncbi_domain=handbook&ncbi_report=record&ncbi_type=fulltext&ncbi_objectid=&ncbi_pcid=/NBK21095/&ncbi_pagename=Macromolecular Structure Databases - The NCBI Handbook - NCBI Bookshelf&ncbi_bookparttype=chapter&ncbi_app=bookshelf" /></noscript>
|
||
|
||
|
||
<!-- usually for JS scripts at page bottom -->
|
||
<!--<component id="PageFixtures" label="styles"></component>-->
|
||
|
||
|
||
<!-- CE8BC1E97D9F05E1_0182SID /projects/books/PBooks@9.11 portal106 v4.1.r689238 Tue, Oct 22 2024 16:10:51 -->
|
||
<span id="portal-csrf-token" style="display:none" data-token="CE8BC1E97D9F05E1_0182SID"></span>
|
||
|
||
<script type="text/javascript" src="//static.pubmed.gov/portal/portal3rc.fcgi/4216699/js/3879255/4121861/3501987/4008961/3893018/3821238/4062932/4209313/4212053/4076480/3921943/3400083/3426610.js" snapshot="books"></script></body>
|
||
</html> |