199 lines
91 KiB
Text
199 lines
91 KiB
Text
<!DOCTYPE html>
|
|
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" class="no-js no-jr">
|
|
<head>
|
|
<!-- For pinger, set start time and add meta elements. -->
|
|
<script type="text/javascript">var ncbi_startTime = new Date();</script>
|
|
|
|
<!-- Logger begin -->
|
|
<meta name="ncbi_db" content="books">
|
|
<meta name="ncbi_pdid" content="book-part">
|
|
<meta name="ncbi_acc" content="NBK453097">
|
|
<meta name="ncbi_domain" content="glyco3">
|
|
<meta name="ncbi_report" content="reader">
|
|
<meta name="ncbi_type" content="fulltext">
|
|
<meta name="ncbi_objectid" content="">
|
|
<meta name="ncbi_pcid" content="/NBK453097/?report=reader">
|
|
<meta name="ncbi_pagename" content="Glycoinformatics - Essentials of Glycobiology - NCBI Bookshelf">
|
|
<meta name="ncbi_bookparttype" content="chapter">
|
|
<meta name="ncbi_app" content="bookshelf">
|
|
<!-- Logger end -->
|
|
|
|
<!--component id="Page" label="meta"/-->
|
|
<script type="text/javascript" src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.boots.min.js"> </script><title>Glycoinformatics - Essentials of Glycobiology - NCBI Bookshelf</title>
|
|
<meta charset="utf-8">
|
|
<meta name="apple-mobile-web-app-capable" content="no">
|
|
<meta name="viewport" content="initial-scale=1,minimum-scale=1,maximum-scale=1,user-scalable=no">
|
|
<meta name="jr-col-layout" content="auto">
|
|
<meta name="jr-prev-unit" content="/books/n/glyco3/ch51/?report=reader">
|
|
<meta name="jr-next-unit" content="/books/n/glyco3/ch53/?report=reader">
|
|
<meta name="bk-toc-url" content="/books/n/glyco3/?report=toc">
|
|
<meta name="robots" content="INDEX,FOLLOW,NOARCHIVE,NOIMAGEINDEX">
|
|
<meta name="citation_inbook_title" content="Essentials of Glycobiology [Internet]. 3rd edition">
|
|
<meta name="citation_title" content="Glycoinformatics">
|
|
<meta name="citation_publisher" content="Cold Spring Harbor Laboratory Press">
|
|
<meta name="citation_date" content="2017">
|
|
<meta name="citation_author" content="Matthew P. Campbell">
|
|
<meta name="citation_author" content="Kiyoko F. Aoki-Kinoshita">
|
|
<meta name="citation_author" content="Frederique Lisacek">
|
|
<meta name="citation_author" content="William S. York">
|
|
<meta name="citation_author" content="Nicolle H. Packer">
|
|
<meta name="citation_pmid" content="28876860">
|
|
<meta name="citation_doi" content="10.1101/glycobiology.3e.052">
|
|
<meta name="citation_fulltext_html_url" content="https://www.ncbi.nlm.nih.gov/books/NBK453097/">
|
|
<link rel="schema.DC" href="http://purl.org/DC/elements/1.0/">
|
|
<meta name="DC.Title" content="Glycoinformatics">
|
|
<meta name="DC.Type" content="Text">
|
|
<meta name="DC.Publisher" content="Cold Spring Harbor Laboratory Press">
|
|
<meta name="DC.Contributor" content="Matthew P. Campbell">
|
|
<meta name="DC.Contributor" content="Kiyoko F. Aoki-Kinoshita">
|
|
<meta name="DC.Contributor" content="Frederique Lisacek">
|
|
<meta name="DC.Contributor" content="William S. York">
|
|
<meta name="DC.Contributor" content="Nicolle H. Packer">
|
|
<meta name="DC.Date" content="2017">
|
|
<meta name="DC.Identifier" content="https://www.ncbi.nlm.nih.gov/books/NBK453097/">
|
|
<meta name="DC.Language" content="en">
|
|
<meta name="description" content="Previous chapters have described how glycans are not directly encoded by genes and that they are biosynthetically and structurally complex. The identity of each glycan in a biological sample must be identified using analytical methods to determine these diverse structural features. As a consequence, research aimed at understanding the biological roles and consequences of glycan structures depends on the availability of databases that allow these structures to be defined, archived, organized, searched, annotated, and linked to other databases with related genomic and proteomic information. This chapter describes the current status of collecting, organizing, and extending data from existing user-entered glycan structure and function databases.">
|
|
<meta name="og:title" content="Glycoinformatics">
|
|
<meta name="og:type" content="book">
|
|
<meta name="og:description" content="Previous chapters have described how glycans are not directly encoded by genes and that they are biosynthetically and structurally complex. The identity of each glycan in a biological sample must be identified using analytical methods to determine these diverse structural features. As a consequence, research aimed at understanding the biological roles and consequences of glycan structures depends on the availability of databases that allow these structures to be defined, archived, organized, searched, annotated, and linked to other databases with related genomic and proteomic information. This chapter describes the current status of collecting, organizing, and extending data from existing user-entered glycan structure and function databases.">
|
|
<meta name="og:url" content="https://www.ncbi.nlm.nih.gov/books/NBK453097/">
|
|
<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-glyco3-lrg.png">
|
|
<meta name="twitter:card" content="summary">
|
|
<meta name="twitter:site" content="@ncbibooks">
|
|
<meta name="bk-non-canon-loc" content="/books/n/glyco3/ch52/?report=reader">
|
|
<link rel="canonical" href="https://www.ncbi.nlm.nih.gov/books/NBK579995/">
|
|
<link href="https://fonts.googleapis.com/css?family=Archivo+Narrow:400,700,400italic,700italic&subset=latin" rel="stylesheet" type="text/css">
|
|
<link rel="stylesheet" href="/corehtml/pmc/jatsreader/ptpmc_3.22/css/libs.min.css">
|
|
<link rel="stylesheet" href="/corehtml/pmc/jatsreader/ptpmc_3.22/css/jr.min.css">
|
|
<meta name="format-detection" content="telephone=no">
|
|
<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">
|
|
<link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books_reader.min.css" type="text/css">
|
|
<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>
|
|
|
|
<link rel="shortcut icon" href="//www.ncbi.nlm.nih.gov/favicon.ico">
|
|
<meta name="ncbi_phid" content="CE8C80CA7D6912C10000000000570048.m_5">
|
|
<meta name='referrer' content='origin-when-cross-origin'/><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4216699/css/3852956/3849091.css"></head>
|
|
<body>
|
|
<!-- Book content! -->
|
|
|
|
|
|
<div id="jr" data-jr-path="/corehtml/pmc/jatsreader/ptpmc_3.22/"><div class="jr-unsupported"><table class="modal"><tr><td><span class="attn inline-block"></span><br />Your browser does not support the NLM PubReader view.<br />Go to <a href="/pmc/about/pr-browsers/">this page</a> to see a list of supported browsers<br />or return to the <br /><a href="/books/NBK453097/?report=classic">regular view</a>.</td></tr></table></div><div id="jr-ui" class="hidden"><nav id="jr-head"><div class="flexh tb"><div id="jr-tb1"><a id="jr-links-sw" class="hidden" title="Links"><svg xmlns="http://www.w3.org/2000/svg" version="1.1" x="0px" y="0px" viewBox="0 0 70.6 85.3" style="enable-background:new 0 0 70.6 85.3;vertical-align:middle" xml:space="preserve" width="24" height="24">
|
|
<style type="text/css">.st0{fill:#939598;}</style>
|
|
<g>
|
|
<path class="st0" d="M36,0C12.8,2.2-22.4,14.6,19.6,32.5C40.7,41.4-30.6,14,35.9,9.8"></path>
|
|
<path class="st0" d="M34.5,85.3c23.2-2.2,58.4-14.6,16.4-32.5c-21.1-8.9,50.2,18.5-16.3,22.7"></path>
|
|
<path class="st0" d="M34.7,37.1c66.5-4.2-4.8-31.6,16.3-22.7c42.1,17.9,6.9,30.3-16.4,32.5h1.7c-66.2,4.4,4.8,31.6-16.3,22.7 c-42.1-17.9-6.9-30.3,16.4-32.5"></path>
|
|
</g>
|
|
</svg> Books</a></div><div class="jr-rhead f1 flexh"><div class="head"><a href="/books/n/glyco3/ch51/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M75,30 c-80,60 -80,0 0,60 c-30,-60 -30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Prev</text></svg></a></div><div class="body"><div class="t">Chapter 52, Glycoinformatics</div><div class="j">Essentials of Glycobiology [Internet]. 3rd edition</div></div><div class="tail"><a href="/books/n/glyco3/ch53/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M25,30c80,60 80,0 0,60 c30,-60 30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Next</text></svg></a></div></div><div id="jr-tb2"><a id="jr-bkhelp-sw" class="btn wsprkl hidden" title="Help with NLM PubReader">?</a><a id="jr-help-sw" class="btn wsprkl hidden" title="Settings and typography in NLM PubReader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" preserveAspectRatio="none"><path d="M462,283.742v-55.485l-29.981-10.662c-11.431-4.065-20.628-12.794-25.274-24.001 c-0.002-0.004-0.004-0.009-0.006-0.013c-4.659-11.235-4.333-23.918,0.889-34.903l13.653-28.724l-39.234-39.234l-28.72,13.652 c-10.979,5.219-23.68,5.546-34.908,0.889c-0.005-0.002-0.01-0.003-0.014-0.005c-11.215-4.65-19.933-13.834-24-25.273L283.741,50 h-55.484l-10.662,29.981c-4.065,11.431-12.794,20.627-24.001,25.274c-0.005,0.002-0.009,0.004-0.014,0.005 c-11.235,4.66-23.919,4.333-34.905-0.889l-28.723-13.653l-39.234,39.234l13.653,28.721c5.219,10.979,5.545,23.681,0.889,34.91 c-0.002,0.004-0.004,0.009-0.006,0.013c-4.649,11.214-13.834,19.931-25.271,23.998L50,228.257v55.485l29.98,10.661 c11.431,4.065,20.627,12.794,25.274,24c0.002,0.005,0.003,0.01,0.005,0.014c4.66,11.236,4.334,23.921-0.888,34.906l-13.654,28.723 l39.234,39.234l28.721-13.652c10.979-5.219,23.681-5.546,34.909-0.889c0.005,0.002,0.01,0.004,0.014,0.006 c11.214,4.649,19.93,13.833,23.998,25.271L228.257,462h55.484l10.595-29.79c4.103-11.538,12.908-20.824,24.216-25.525 c0.005-0.002,0.009-0.004,0.014-0.006c11.127-4.628,23.694-4.311,34.578,0.863l28.902,13.738l39.234-39.234l-13.66-28.737 c-5.214-10.969-5.539-23.659-0.886-34.877c0.002-0.005,0.004-0.009,0.006-0.014c4.654-11.225,13.848-19.949,25.297-24.021 L462,283.742z M256,331.546c-41.724,0-75.548-33.823-75.548-75.546s33.824-75.547,75.548-75.547 c41.723,0,75.546,33.824,75.546,75.547S297.723,331.546,256,331.546z"></path></svg></a><a id="jr-fip-sw" class="btn wsprkl hidden" title="Find"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 550 600" preserveAspectRatio="none"><path fill="none" stroke="#000" stroke-width="36" stroke-linecap="round" style="fill:#FFF" d="m320,350a153,153 0 1,0-2,2l170,170m-91-117 110,110-26,26-110-110"></path></svg></a><a id="jr-rtoc-sw" class="btn wsprkl hidden" title="Table of Contents"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M20,20h10v8H20V20zM36,20h44v8H36V20zM20,37.33h10v8H20V37.33zM36,37.33h44v8H36V37.33zM20,54.66h10v8H20V54.66zM36,54.66h44v8H36V54.66zM20,72h10v8 H20V72zM36,72h44v8H36V72z"></path></svg></a></div></div></nav><nav id="jr-dash" class="noselect"><nav id="jr-dash" class="noselect"><div id="jr-pi" class="hidden"><a id="jr-pi-prev" class="hidden" title="Previous page"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M75,30 c-80,60 -80,0 0,60 c-30,-60 -30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Prev</text></svg></a><div class="pginfo">Page <i class="jr-pg-pn">0</i> of <i class="jr-pg-lp">0</i></div><a id="jr-pi-next" class="hidden" title="Next page"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M25,30c80,60 80,0 0,60 c30,-60 30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Next</text></svg></a></div><div id="jr-is-tb"><a id="jr-is-sw" class="btn wsprkl hidden" title="Switch between Figures/Tables strip and Progress bar"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><rect x="10" y="40" width="20" height="20"></rect><rect x="40" y="40" width="20" height="20"></rect><rect x="70" y="40" width="20" height="20"></rect></svg></a></div><nav id="jr-istrip" class="istrip hidden"><a id="jr-is-prev" href="#" class="hidden" title="Previous"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M80,40 60,65 80,90 70,90 50,65 70,40z M50,40 30,65 50,90 40,90 20,65 40,40z"></path><text x="35" y="25" textLength="60" style="font-size:25px">Prev</text></svg></a><a id="jr-is-next" href="#" class="hidden" title="Next"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M20,40 40,65 20,90 30,90 50,65 30,40z M50,40 70,65 50,90 60,90 80,65 60,40z"></path><text x="15" y="25" textLength="60" style="font-size:25px">Next</text></svg></a></nav><nav id="jr-progress"></nav></nav></nav><aside id="jr-links-p" class="hidden flexv"><div class="tb sk-htbar flexh"><div><a class="jr-p-close btn wsprkl">Done</a></div><div class="title-text f1">NCBI Bookshelf</div></div><div class="cnt lol f1"><a href="/books/">Home</a><a href="/books/browse/">Browse All Titles</a><a class="btn share" target="_blank" rel="noopener noreferrer" href="https://www.facebook.com/sharer/sharer.php?u=https://www.ncbi.nlm.nih.gov/books/NBK453097/"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 33 33" style="vertical-align:middle" width="24" height="24" preserveAspectRatio="none"><g><path d="M 17.996,32L 12,32 L 12,16 l-4,0 l0-5.514 l 4-0.002l-0.006-3.248C 11.993,2.737, 13.213,0, 18.512,0l 4.412,0 l0,5.515 l-2.757,0 c-2.063,0-2.163,0.77-2.163,2.209l-0.008,2.76l 4.959,0 l-0.585,5.514L 18,16L 17.996,32z"></path></g></svg> Share on Facebook</a><a class="btn share" target="_blank" rel="noopener noreferrer" href="https://twitter.com/intent/tweet?url=https://www.ncbi.nlm.nih.gov/books/NBK453097/&text=Glycoinformatics"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 33 33" style="vertical-align:middle" width="24" height="24"><g><path d="M 32,6.076c-1.177,0.522-2.443,0.875-3.771,1.034c 1.355-0.813, 2.396-2.099, 2.887-3.632 c-1.269,0.752-2.674,1.299-4.169,1.593c-1.198-1.276-2.904-2.073-4.792-2.073c-3.626,0-6.565,2.939-6.565,6.565 c0,0.515, 0.058,1.016, 0.17,1.496c-5.456-0.274-10.294-2.888-13.532-6.86c-0.565,0.97-0.889,2.097-0.889,3.301 c0,2.278, 1.159,4.287, 2.921,5.465c-1.076-0.034-2.088-0.329-2.974-0.821c-0.001,0.027-0.001,0.055-0.001,0.083 c0,3.181, 2.263,5.834, 5.266,6.438c-0.551,0.15-1.131,0.23-1.73,0.23c-0.423,0-0.834-0.041-1.235-0.118 c 0.836,2.608, 3.26,4.506, 6.133,4.559c-2.247,1.761-5.078,2.81-8.154,2.81c-0.53,0-1.052-0.031-1.566-0.092 c 2.905,1.863, 6.356,2.95, 10.064,2.95c 12.076,0, 18.679-10.004, 18.679-18.68c0-0.285-0.006-0.568-0.019-0.849 C 30.007,8.548, 31.12,7.392, 32,6.076z"></path></g></svg> Share on Twitter</a></div></aside><aside id="jr-rtoc-p" class="hidden flexv"><div class="tb sk-htbar flexh"><div><a class="jr-p-close btn wsprkl">Done</a></div><div class="title-text f1">Table of Content</div></div><div class="cnt lol f1"><a href="/books/n/glyco3/?report=reader">Title Information</a><a href="/books/n/glyco3/toc/?report=reader">Table of Contents Page</a></div></aside><aside id="jr-help-p" class="hidden flexv"><div class="tb sk-htbar flexh"><div><a class="jr-p-close btn wsprkl">Done</a></div><div class="title-text f1">Settings</div></div><div class="cnt f1"><div id="jr-typo-p" class="typo"><div><a class="sf btn wsprkl">A-</a><a class="lf btn wsprkl">A+</a></div><div><a class="bcol-auto btn wsprkl"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 200 100" preserveAspectRatio="none"><text x="10" y="70" style="font-size:60px;font-family: Trebuchet MS, ArialMT, Arial, sans-serif" textLength="180">AUTO</text></svg></a><a class="bcol-1 btn wsprkl"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M15,25 85,25zM15,40 85,40zM15,55 85,55zM15,70 85,70z"></path></svg></a><a class="bcol-2 btn wsprkl"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M5,25 45,25z M55,25 95,25zM5,40 45,40z M55,40 95,40zM5,55 45,55z M55,55 95,55zM5,70 45,70z M55,70 95,70z"></path></svg></a></div></div><div class="lol"><a class="" href="/books/NBK453097/?report=classic">Switch to classic view</a><a href="/books/NBK453097/?report=printable">Print View</a></div></div></aside><aside id="jr-bkhelp-p" class="hidden flexv"><div class="tb sk-htbar flexh"><div><a class="jr-p-close btn wsprkl">Done</a></div><div class="title-text f1">Help</div></div><div class="cnt f1 lol"><a id="jr-helpobj-sw" data-path="/corehtml/pmc/jatsreader/ptpmc_3.22/" data-href="/corehtml/pmc/jatsreader/ptpmc_3.22/img/bookshelf/help.xml" href="">Help</a><a href="mailto:info@ncbi.nlm.nih.gov?subject=PubReader%20feedback%20%2F%20NBK453097%20%2F%20sid%3ACE8B5AF87C7FFCB1_0191SID%20%2F%20phid%3ACE8C80CA7D6912C10000000000570048.4">Send us feedback</a><a id="jr-about-sw" data-path="/corehtml/pmc/jatsreader/ptpmc_3.22/" data-href="/corehtml/pmc/jatsreader/ptpmc_3.22/img/bookshelf/about.xml" href="">About PubReader</a></div></aside><aside id="jr-objectbox" class="thidden hidden"><div class="jr-objectbox-close wsprkl">✘</div><div class="jr-objectbox-inner cnt"><div class="jr-objectbox-drawer"></div></div></aside><nav id="jr-pm-left" class="hidden"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 40 800" preserveAspectRatio="none"><text font-stretch="ultra-condensed" x="800" y="-15" text-anchor="end" transform="rotate(90)" font-size="18" letter-spacing=".1em">Previous Page</text></svg></nav><nav id="jr-pm-right" class="hidden"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 40 800" preserveAspectRatio="none"><text font-stretch="ultra-condensed" x="800" y="-15" text-anchor="end" transform="rotate(90)" font-size="18" letter-spacing=".1em">Next Page</text></svg></nav><nav id="jr-fip" class="hidden"><nav id="jr-fip-term-p"><input type="search" placeholder="search this page" id="jr-fip-term" autocorrect="off" autocomplete="off" /><a id="jr-fip-mg" class="wsprkl btn" title="Find"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 550 600" preserveAspectRatio="none"><path fill="none" stroke="#000" stroke-width="36" stroke-linecap="round" style="fill:#FFF" d="m320,350a153,153 0 1,0-2,2l170,170m-91-117 110,110-26,26-110-110"></path></svg></a><a id="jr-fip-done" class="wsprkl btn" title="Dismiss find">✘</a></nav><nav id="jr-fip-info-p"><a id="jr-fip-prev" class="wsprkl btn" title="Jump to previuos match">◀</a><button id="jr-fip-matches">no matches yet</button><a id="jr-fip-next" class="wsprkl btn" title="Jump to next match">▶</a></nav></nav></div><div id="jr-epub-interstitial" class="hidden"></div><div id="jr-content"><article data-type="main"><p class="vip-notice"><strong><a href="/books/n/glyco4/?report=reader">A new version of this title is available</a></strong></p><p class="vip-notice"><strong><a href="/books/NBK579995/?report=reader">See the updated version of this chapter</a></strong></p><div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><div class="fm-sec"><h1 id="_NBK453097_"><span class="label">Chapter 52</span><span class="title" itemprop="name">Glycoinformatics</span></h1><p class="contribs">Campbell MP, Aoki-Kinoshita KF, Lisacek F, et al.</p><p class="fm-aai"><a href="#_NBK453097_pubdet_">Publication Details</a></p></div></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="_abs_rndgid_" itemprop="description"><p>Previous chapters have described how glycans are not directly encoded by genes and that they are biosynthetically and structurally complex. The identity of each glycan in a biological sample must be identified using analytical methods to determine these diverse structural features. As a consequence, research aimed at understanding the biological roles and consequences of glycan structures depends on the availability of databases that allow these structures to be defined, archived, organized, searched, annotated, and linked to other databases with related genomic and proteomic information. This chapter describes the current status of collecting, organizing, and extending data from existing user-entered glycan structure and function databases.</p></div><div id="Ch52_s1"><h2 id="_Ch52_s1_">THE NEED FOR INFORMATICS IN GLYCOBIOLOGY</h2><p>Informatics plays a critical role in virtually every aspect of modern biology. Our ability to compile the genomes of diverse organisms makes it possible to predict the sequences of the proteins made by these organisms. These sequences are widely used as the basis to predict protein function and to enable proteomic analyses. Proteomic studies in turn advance biological research by providing experimental evidence that supports the expression of specific proteins, in particular tissues or cell types (<a class="figpopup" href="/books/NBK453097/figure/ch52.f1/?report=objectonly" target="object" rid-figpopup="figch52f1" rid-ob="figobch52f1">Figure 52.1</a>). The informatics resources that support these endeavors are facilitated by the fact that genes and the translated polypeptides (i.e., proteins) are typically linear molecules whose sequences are readily specified as a series of characters. These representations are easy to digitize and store and many powerful informatics tools for comparing and classifying polypeptides have been developed. In contrast, the development of informatics tools for glycobiology is much more difficult for several reasons. Notably, glycans are not directly encoded by genes. Rather, each sugar residue in a growing glycan is added by a distinct enzyme (i.e., a glycosyltransferase [GT]) (<a href="/books/n/glyco3/ch6/?report=reader">Chapter 6</a>). These reactions are tightly controlled by the availability of the donor and acceptor substrates in the cellular compartment containing the GT. In addition, the organization and function of the endoplasmic reticulum (ER)–Golgi biosynthetic pathway is sensitive to many factors such as the metabolic or developmental stage of the cell, or its level of nutrients (<a href="/books/n/glyco3/ch4/?report=reader">Chapter 4</a>) and leads to structures that can be extremely complex (<a href="/books/n/glyco3/ch3/?report=reader">Chapter 3</a>). Furthermore, complex glycans are often highly branched and their structures cannot be described as a simple linear sequence (<a href="/books/n/glyco3/ch3/?report=reader">Chapter 3</a>).</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figch52f1" co-legend-rid="figlgndch52f1"><a href="/books/NBK453097/figure/ch52.f1/?report=objectonly" target="object" title="FIGURE 52.1." class="img_link icnblk_img figpopup" rid-figpopup="figch52f1" rid-ob="figobch52f1"><img class="small-thumb" src="/books/NBK453097/bin/ch52f01.gif" src-large="/books/NBK453097/bin/ch52f01.jpg" alt="FIGURE 52.1.. The critical role of glycomics in systems biology." /></a><div class="icnblk_cntnt" id="figlgndch52f1"><h4 id="ch52.f1"><a href="/books/NBK453097/figure/ch52.f1/?report=objectonly" target="object" rid-ob="figobch52f1">FIGURE 52.1.</a></h4><p class="float-caption no_bottom_margin">The critical role of glycomics in systems biology. Glycan structures have no template from which to be predicted, are regulated by cellular metabolism and glyco-enzyme expression, and modify both proteins and lipids. Glycomics thus requires the tools <a href="/books/NBK453097/figure/ch52.f1/?report=objectonly" target="object" rid-ob="figobch52f1">(more...)</a></p></div></div><p>Because of this biosynthetic and structural complexity, it is not currently possible to accurately predict the structures of the glycans that an organism can produce or how these glycans are conjugated with other molecules, armed only with knowledge of that organism's genome or proteome. Rather, the identity of each glycan in a biological sample must be identified using analytical methods (<a href="/books/n/glyco3/ch50/?report=reader">Chapters 50</a> and <a href="/books/n/glyco3/ch51/?report=reader">51</a>) that are sufficiently sophisticated to detect and discern the glycan's diverse structural features. Thus, research aimed at understanding the biological roles and consequences of glycan structures depends on the availability of databases that allow these structures to be archived, organized, searched, and annotated. However, the complexity and diversity of glycan structures make the development of these databases challenging. Currently there is no way to accurately predict the entire biological complement of glycan structures in Nature, and so different approaches are being used to create comprehensive databases. Collecting, organizing, and extending data from existing user-entered glycan structure databases, curating the available literature on described structures, and developing a “virtual” database by predicting possible structures based on the described synthetic pathways, are all ways in which this challenge is presently being addressed.</p><p>Interpreting glycan structural information in the context of diverse types of biological and chemical information is an additional challenge. For example, most glycans in animals are covalently linked to proteins or lipids. The glycan moieties of a glycoprotein are linked to specific amino acids (usually asparagine, serine, or threonine) (<a href="/books/n/glyco3/ch9/?report=reader">Chapters 9</a> and <a href="/books/n/glyco3/ch10/?report=reader">10</a>). Which sites are glycosylated and which structures are present at a particular site often vary, depending on many factors, including the type, developmental stage, and disease state of the cell or tissue. Collection, storage, and retrieval of a description of each protein's glycosylation is time-, tissue-, organism-, interaction-, and disease-dependent and thus presents a major challenge to bioinformaticians working in the glycosciences (glycoinformaticians) as it requires integration of conceptually diverse information, which may be stored in several different data repositories and represented in various formats. Several distinct digital formats have been used by existing databases to describe glycan structures. However, these formats have diverged to become quite distinct, making it difficult to compare information from different databases. This situation demands the establishment of standard digital formats to represent this diverse information such that it can be retrieved, parsed, and manipulated by computational and visualization tools, thus making it easier for the scientist to comprehend this complex information. For glycoproteins, the structures of both the glycan and the protein must be represented along with the relationship between these two entities (e.g., the identity of the glycosylation site and the fraction of the protein molecules that bear the glycan in each physiological state). To make this information relevant, the scientist often requires explicit information about the biological context (e.g., tissue and disease state) corresponding to the specified glycosylation or describing how the glycosylation changes when the tissue or cell is perturbed. The glycoscience community is building on the Human Proteome Organization-Proteomics Standards Initiative (HUPO-PSI) foundations to develop similar resources that describe the information that should be included when reporting experimental data, with digital data exchange formats to facilitate communication of structural and biological information and controlled vocabularies that allow the data that is exchanged to be unambiguously interpreted. For example, the Minimum Information Required for A Glycomics Experiment (MIRAGE) initiative (see below) is modeled after the well-established Minimum Information for A Proteomics Experiment (MIAPE) initiative of HUPO-PSI. These standards are required for the emergence of glycobiology as a mature discipline that is accessible to the scientific community as a whole.</p><p>Databases that provide authoritative information about glycan and glycoconjugate structures, and well-defined standards that allow this information to be exchanged, are required as a foundation for computational tools that give insight into the biological functions and consequences of glycosylation. Many different types of digital tools are necessary, ranging from basic visualization software to software that assists in the interpretation and structural annotation of glycoanalytic data (e.g., mass spectra), to algorithms that identify correlations between glycosylation and other biological phenomena (e.g., gene expression, disease, cell differentiation). A major challenge facing the glycoinformatician is the representation of the information that is consumed and produced by these software tools in ways that are conceptually accessible to scientists who do not have an extensive background in glycobiology. Eventually all data needs to be permanently housed at long-term government-funded sites such as the <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">National Center for Biotechnology Information (NCBI)</a> and the <a href="http://www.ebi.ac.uk" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">European Bioinformatics Institute (EBI)</a>. Needless to say, glycoinformaticians have their work cut out for them.</p></div><div id="Ch52_s2"><h2 id="_Ch52_s2_">PAST AND PRESENT EFFORTS</h2><p>The Complex Carbohydrate Structure Database (CCSD) (commonly referred to as CarbBank) was established in the mid-1980s and was developed and maintained by the Complex Carbohydrate Research Center of the University of Georgia (USA). The main design objective of CCSD was to allow researchers to find publications in which specific carbohydrate structures were reported. The need to develop CarbBank as an international effort was clearly recognized and resulted in worldwide curation teams responsible for specific classes of glycans that resulted in more than 30,000 entries into the database. During the 1990s, a Dutch group (led by Hans Vliegenthart) assigned nuclear magnetic resonance (NMR) spectra to CCSD entries (SugaBase). This was the first attempt to create a carbohydrate NMR database that complemented CCSD entries with proton and carbon chemical shift values. Unfortunately, funding for CCSD was discontinued in 1997. Several large projects have followed, among which was EUROCarbDB, but it ceased operation in 2011. EUROCarbDB was a design study initiated to develop an infrastructure for carbohydrate-related data (structure and function), comparable to and cross-linked with the extensively used genomics and proteomics data collections. The initiative seeded integrated tools for streamlining European glycomics research through the development of databases, bioinformatics standards, efficient analysis and search algorithms, and Web-based software components.</p><p>During this period, the Australian company, Proteome Systems, provided commercial access to mammalian N- and O-glycan structures and glycoprotein data curated from the literature in GlycoSuiteDB. The last release of GlycoSuiteDB comprised more than 3000 glycoprotein-derived glycan structure entries and relevant metadata descriptors including taxonomy, disease, and methods of determination. This effort to provide curated information at the glycoprotein level now continues under the UniCarbKB initiative.</p><p>In 2001, the Consortium for Functional Glycomics (CFG) was established, under the support of the U.S. National Institute of General Medical Sciences, with the objective to deepen the understanding of the function of carbohydrate–protein interactions on the cell surface and in cell–cell communication. The CFG generated diverse data sets which were derived from (1) gene expression of glycosyltransferases and glycan-binding proteins (GBPs), (2) phenotypic analysis of transgenic mice, (3) mass spectrometric profiling of glycan structures isolated from cells and tissues, and (4) screening glycan affinity of proteins using glycan arrays.</p><p>Multiple initiatives to organize various glycan-related information and resources have been launched over the last couple of decades since CarbBank: GLYCOSCIENCES.de, CFG, EUROCarbDB, Kyoto Encyclopedia of Genes and Genomes (KEGG) GLYCAN, Bacterial Carbohydrate Structure Database (BCSDB), Japan Consortium for Glycobiology and Glycotechnology Database (JCGGDB), UniCarbKB, and GlycomeDB, among other established programs. <a class="figpopup" href="/books/NBK453097/table/CH52TB1/?report=objectonly" target="object" rid-figpopup="figCH52TB1" rid-ob="figobCH52TB1">Table 52.1</a> provides a list of software tools that are currently available across the areas of structure databases, ontologies and guidelines, analytical tools, glyco-enzymes, glycan binding, and three-dimensional (3D)/modeling/nuclear magnetic resonance (NMR).</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figCH52TB1"><a href="/books/NBK453097/table/CH52TB1/?report=objectonly" target="object" title="TABLE 52.1." class="img_link icnblk_img figpopup" rid-figpopup="figCH52TB1" rid-ob="figobCH52TB1"><img class="small-thumb" src="/books/NBK453097/table/CH52TB1/?report=thumb" src-large="/books/NBK453097/table/CH52TB1/?report=previmg" alt="TABLE 52.1." /></a><div class="icnblk_cntnt"><h4 id="CH52TB1"><a href="/books/NBK453097/table/CH52TB1/?report=objectonly" target="object" rid-ob="figobCH52TB1">TABLE 52.1.</a></h4><p class="float-caption no_bottom_margin">List of available glycoscience-related informatics </p></div></div></div><div id="Ch52_s3"><h2 id="_Ch52_s3_">ACCUMULATION VERSUS CURATION</h2><p>An important question is, what constitutes a glycan structure database useful to all biologists? Current databases are largely incomplete and have a significant number of incorrect entries that have accumulated. Many errors are due to a lack of sufficient curation.</p><p>GlycomeDB was an initiative (by Rene Ranzinger) to consolidate structures from a number of established glycan structure databases and provide links to the original sources. A challenge has been the maintenance of GlycomeDB, which required continuous updates to the data whenever one of the original databases is updated. GlyTouCan (see below) was recently established as a stable repository of chemically valid glycan structures and associated accession numbers that can be used by diverse glycobiology data systems and has replaced GlycomeDB in this context. Structures stored in GlyTouCan are checked only for representational and chemical consistency and not for biological relevance. Thus, databases that leverage GlyTouCan structural representations still require improved methods for establishing and validating the biological context of these structures. It should be noted that, because of the reliance on analytical structure determination, a limitation for a majority of databases is the number of fully characterized entries (i.e., defined linkages and anomeric configurations between monosaccharides). For example, less than 15,000 out of the 40,000 structures in the amalgamated GlycomeDB are fully defined.</p><p>Another approach to establish a glycan structure database is to scour the published scientific literature for information. In 2010, the content of GlycoSuiteDB was migrated into the UniCarbKB database, which provides a series of new user interfaces and functionalities and has been made accessible and linked to protein data on the SIB (Swiss Institute of Bioinformatics) ExPASy proteomics server.</p><p>KEGG GLYCAN, part of KEGG, was originally developed to store glycan structural data and related pathway information (KEGG PATHWAY), and similar to other databases, contains glycan structures extracted from CarbBank and structures curated from the literature. However, because of the limited amount of data at the time, a tool was developed to generate a virtual N-glycan structure database (UniCorn; <a href="http://www.unicarbkb.org/unicorn" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www.unicarbkb.org/unicorn</a>), facilitated by the Resource for Informatics of Glycomes at Soka (RINGS) resource Glycan Pathway Predictor (GPP) tool. This tool generates, on-the-fly, all potential glycan structures that can be synthesized starting from a specific glycan structure and using a selection of enzymes involved in N<i>-</i>glycan biosynthesis with the known substrate specificity information for each glyco-enzyme. All of the possible glycans that could be synthesized can then be computationally generated to obtain a library of N-glycans that could be theoretically found in a particular cell. This approach is dependent on the currently available information on the activity and specificities of the selected enzymes.</p><p>It should be noted that most of these described efforts are focused on vertebrate oligosaccharides. The Carbohydrate Structure Database (CSDB) is the leading curated platform for bacterial, archaeal, plant, and fungal carbohydrates containing more than 160,000 compounds from 7700 organisms. CSDB provides structural, bibliographic, taxonomic, NMR, and other related information on carbohydrate structures, curated from the literature.</p><p>Several other glycodatabases are dedicated to knowledge of proteins that are either involved in the synthesis/degradation of glycans or in their recognition. The Carbohydrate-Active Enzymes (CAZy) database records carbohydrate-related enzymes based on taxonomy and an internal classification scheme relying on amino acid sequence profiles (<a href="/books/n/glyco3/ch8/?report=reader">Chapter 8</a>). Since 1998, the number of glyco-enzyme families has continued to grow to reach several hundreds. CAZy links to reference sequence databases as well as to Protein Data Bank (PDB) three-dimensional protein structures. Lectin databases have also been developed over the years, although they remain with low content, reflecting the technical challenges in collecting information regarding these proteins (e.g., LectinDB and Lectin Frontier DB).</p></div><div id="Ch52_s4"><h2 id="_Ch52_s4_">STANDARDIZATION AND ONTOLOGIES</h2><p>A critical component of glycoinformatics is the availability of standardized approaches to connect remote databases. To address this problem a number of international efforts are underway to establish standards for the presentation of glycomics data to facilitate data comparison, exchange, and verification, which in turn simplifies cross-linking across individual glycan databases.</p><p>The Glycomics Ontology (GlycO) was the first ontology developed to provide standard terminologies for representing experimentally verified glycan structures. Another effort, GlycoRDF, is a proposed standard ontology for glycomics data using Resource Description Framework (RDF) to provide consistent terminologies for representing glycan sequences, related biological sources, publications, and experimental data on the Semantic Web. GlycoRDF is now being used by several glycomics database providers, to enable large-scale integration of diverse data collections in the glycosciences.</p><p>The essential accurate interpretation of glycoanalytical data for glycan structure determination requires well-documented metadata, including the parameters used to acquire and process the raw data along with supporting biological source information for the sample being analyzed. Since 2011, the glycomics community has supported the MIRAGE initiative to develop guidelines for researchers to report the qualitative and quantitative results obtained by diverse types of glycomics analyses (e.g., chromatography, mass spectrometry, and arrays).</p><p>The establishment of unique identifiers for each glycan structure is the first step toward the collection and organization of structural data, and a glycan structure repository of structure identifiers for all structures—from fully defined to incompletely specified or purely hypothetical—is needed. These unique identifiers provide the semantic foundation required for individuals or databases to effectively communicate by recording the identifier of the structures they have characterized. A glycan registry allows precise specification of the structural features that support the data, and unique identifiers can be assigned to each partly or fully defined structure. This registry facilitates the interpretation of results in the context of structural and biological information that is available from other sources. Nevertheless, a comparison of incompletely defined structures in terms of sequence, linkage, and anomericity remains an ongoing challenge for glycoinformaticians.</p><p>The development of such a repository (GlyTouCan) has begun, promising to provide both developers and researchers with a platform for assigning glycan structures that will connect experimental and curated databases. This repository is a freely available, uncurated registry for glycan structures that assigns globally unique accession numbers to any structure entry. Registered users can submit any glycan structure whether they are fully defined, contain ambiguous linkages, or are simply monosaccharide compositions, independent of experimental evidence. GlyTouCan uses the GlycoRDF ontology to represent the registered data such that other data resources also using this ontology can be integrated and queried by glycan structure. Different information resources (e.g., databases and publications) can reference these identifiers, thus facilitating identification and interpretation of diverse but complementary data sets that embody information about specific glycan structures.</p></div><div id="Ch52_s5"><h2 id="_Ch52_s5_">SOFTWARE TOOLS FOR EXPERIMENTAL DATA INTERPRETATION</h2><p>Many advances in glyco-related databases and informatics tools development have focused on the interpretation and storage of analytical data, including liquid chromatography, capillary electrophoresis, interaction arrays, mass spectrometry (MS), and NMR.</p><div id="Ch52_s5a"><h3>Mass Spectrometry</h3><p>Most efforts so far have focused on tools that assist the interpretation of MS data. A number of commercial and publicly accessible software are now available. Introduced in 1999, the widely used GlycoMod was the first glycoinformatics Web-based tool to be released in this context, and its function is to suggest possible glycan compositions from experimental mass values of either free or derivatized glycans or glycopeptides. The Glycosciences.de portal started a toolset for analyzing and interpreting experimental data, and a decade later, the EUROCarbDB initiative launched GlycoWorkbench as a freely downloadable software tool to assist the interpretation of MS/MS data by matching a theoretical list of fragment masses against the experimental peak list derived from the mass spectrum. This tool has been integrated into several glycan resources as it provides an easy-to-use interface, a comprehensive collection of fragmentation types, and a list of annotation options. UniCarb-DB adopts the approach of storing annotated and curated experimental MS/MS data against which spectral matching can be used to identify unknown structures. RINGS provides Web-based software (Glycan Miner Tool, ProfilePSTMM) to analyze distinguishable glycan fragments from glycan profiling (MS) data, and the GlycomeAtlas tool in RINGS is a visualization tool for glycan profiling data in mouse and human, where the distribution of glycans across various tissues is visualized.</p><p>The GRITS toolbox is also a freely available integrated environment for processing glycoanalytic data. It uses a plug-in approach to facilitate reuse and integration of data-processing modules. Currently, GRITS includes modules for collecting, annotating, and comparing mass spectral data, manipulating the corresponding metadata, and generating reports.</p><p>A major component of GlycoWorkBench is GlycanBuilder, a tool that allows for the drawing of glycan structures. GlycanBuilder can be used stand-alone, embedded in webpages, and can also be integrated into other programs. Recently, an updated version of the tool was included in the UniCarbKB and GlyTouCan databases providing an intuitive method for searching structural content. In-built features provide support for the conversion of various glycan display and formats allowing users to efficiently switch between Essentials/CFG, Oxford, hybrid, and International Union of Pure and Applied Chemistry (IUPAC) symbol formats while supporting different text formats: LinearCode(r), KCF (KEGG Chemical Function), GlycoCT, GLYDE-II, Oxford, and LINUCS. A universal symbol nomenclature for the graphical representation of glycan structures (Symbol Nomenclature for Glycans [SNFG], see <a href="/books/n/glyco3/symbolnomenclature/?report=reader">Online Appendix 1B</a>) has been proposed to facilitate the standardization of how glycans are visually depicted, and is used throughout this book. <a href="/books/n/glyco3/app_snfg_adopt/?report=reader">Online Appendix 52A</a> lists current databases and journal publishers that have thus far accepted or strongly recommend the use of this nomenclature.</p><p>A more recent advancement in glycosciences is the field of glycoproteomics, in which glycoproteins and glycopeptides are analyzed in their native form, with glycans attached to them, using MS techniques (<a class="figpopup" href="/books/NBK453097/figure/ch52.f1/?report=objectonly" target="object" rid-figpopup="figch52f1" rid-ob="figobch52f1">Figure 52.1</a>; <a href="/books/n/glyco3/ch51/?report=reader">Chapter 51</a>). Glycoproteomics not only allows the identification of the glycoprotein and the attached glycans, but also preserves the microheterogeneity information on the glycan structures. Different fragmentation methods (electron transfer dissociation [ETD], collision-induced dissociation [CID], and higher-energy collision dissociation [HCD]) each provide distinct information about the different structural features of glycoproteins. Mass spectrum matching algorithms use a wide range of strategies (e.g., database search, de novo sequencing, or spectral library matching) to identify specific spectral fragment masses and thereby assign glycopeptide structural features. Following the ability now to obtain large data sets on glycopeptides generated from complex mixtures of glycoproteins (<a href="/books/n/glyco3/ch51/?report=reader">Chapter 51</a>), a bottleneck that has severely limited the field of glycoproteomics is the downstream glycopeptide structural identification. The identification process was, until recently, largely driven by manual expert annotation of the resulting MS/MS spectra. However, many glycoinformatics initiatives are under continuing development to automate this glycopeptide identification process using various strategies to identify intact glycopeptides by using characteristic fragment ions. A few software tools are freely available to address the challenge of analyzing glycoproteomics data, such as GlycoMaster DB, Sweet-Heart, GlyPID, GP Finder, and GPQuest, and recent commercial and open-source software developments include Byonic, Protein Prospector, and Skyline that allow semiautomated identification of N- and O-glycopeptides from high-resolution MS/MS data.</p></div><div id="Ch52_s5b"><h3>Liquid Chromatography</h3><p>In comparison to MS, few software tools are available for supporting (ultra)high-performance liquid chromatography (U/HPLC) data analysis and storage. GlycoBase is a Web-enabled proprietary resource that contains normalized chromatographic retention data, expressed as glucose units, for more than 700 fluorescently labeled (2-AB) N-linked and O<i>-</i>linked glycan structures. These values were obtained by systematic analysis of released glycans from a diverse set of mammalian glycoproteins. GlycoBase is supported by a selection of data analysis tools, notably autoGU, which can be used to assign putative glycan structures to each U/HPLC peak, and when used in combination with exoglycosidases creates a digest footprint—that is, using shifts in GU values due to cleavage of terminal monosaccharides to accurately identify and quantitatively analyze a glycan mixture (<a href="/books/n/glyco3/ch51/?report=reader">Chapter 51</a>). This approach has now been commercialized.</p></div><div id="Ch52_s5c"><h3>Nuclear Magnetic Resonance Spectroscopy</h3><p>NMR data was obtained on carbohydrate structures in the 1980s and 1990s and is still the best analytical technique available to obtain complete structural information on purified oligosaccharides but is less used now because of the difficulty in obtaining sufficient material from biological sources. The CASPER (Computer Assisted Spectrum Evaluation of Regular Polysaccharides) program predicts <sup>1</sup>H- and <sup>13</sup>C-NMR chemical shifts of glycans. As such, it is used for determining the glycan structures based on experimental NMR data.</p></div><div id="Ch52_s5d"><h3>Glycan-Binding Data Interpretation</h3><p>Another area of software analysis of experimental data has been in mining glycan array data sets to identify glycan sequence motifs recognized by various GBPs, such as plant and animal lectins, viral and bacterial pathogen proteins, and antibodies. GlycoPattern is a Web-based platform that was developed to support the analysis of CFG glycan array data. It offers a variety of algorithms and tools to mine array data to discover structural binding motifs of GBPs. Such data analysis determines the relative binding strength/specificity of a GBP to a glycan motif or determinant on the array. SugarBind is a curated database that combines this information with literature-derived knowledge of pathogen–glycan binding. RINGS also has analytical tools for predicting glycan-binding patterns from glycan array data.</p></div><div id="Ch52_s5e"><h3>3D Glycan Structure Modeling</h3><p>Because of their inherent flexibility, oligosaccharides typically exist in solution, or on proteins, as an ensemble of conformations, making it a challenge to describe their 3D structure. Computational chemistry is an essential tool in analyzing glycan experimental data, to make predictions that may be tested experimentally and to unravel and explain chemical processes at the atomic level.</p><p>Freely available Web-based tools are available to generate a theoretical model of a carbohydrate 3D structure. A useful resource is GLYCAM-Web that provides tools for modeling oligosaccharides and glycoproteins in addition to providing downloadable structure files that can be used for molecular modeling. SWEET-II is also a carbohydrate 3D builder that is available on the GLYCO SCIENCES.de website.</p><p>The two major databases for storing experimentally determined 3D carbohydrate structures are the PDB and the Cambridge Structural Database. Crystal structures of oligosaccharides and lectins are also available at Glyco3D. Most of the carbohydrates in the PDB are either connected covalently to a glycoprotein, or form a complex with a lectin, enzyme, or antibody. However, because of the absence of sophisticated tools to experimentally determine the 3D shape of glycans and for checking the accuracy of their atomic coordinates in structural data files, it must be noted that PDB does not contain accurate information about carbohydrate stereochemistry, possibly leading to incorrect glycan structure assignments. Statistical analysis of the carbohydrates present in the PDB entries can be performed with tools such as GlyVicinity, and validation/checking of certain glycan structures can be performed with PDB-Care.</p></div><div id="Ch52_s5f"><h3>Glycan Attachment Sites on Proteins</h3><p>Despite the known sequon (NXT/S) for N-linked glycosylation, many potential sites are not glycosylated in vivo, and there are no clear motif(s) for predicting O-linked glycosylation. Understanding the “rules” of attachment site specificity for the glycosylation of proteins is thus an ongoing challenge for glycoinformaticians. Over the past 20 years neural networks, hidden Markov models (HMMs), and support vector machines (SVMs) have been implemented to predict N- or O-glycosylation and C-mannosylation. Most of these tools are hosted on the Danish CBS Prediction Servers. For O-GlcNAcylation sites, a specific SVM-based tool is integrated in dbOGAP where O-GlcNAcylated proteins are collected and curated.</p></div></div><div id="Ch52_s6"><h2 id="_Ch52_s6_">INTERDISCIPLINARY EFFORTS</h2><p>There is tremendous value in integrating genomics, transcriptomics, and proteomics data with glycomics to gain a holistic understanding of a biological process (<a class="figpopup" href="/books/NBK453097/figure/ch52.f1/?report=objectonly" target="object" rid-figpopup="figch52f1" rid-ob="figobch52f1">Figure 52.1</a>). This means that glycomics data needs to be viewed in the context of complementary gene, protein, and lipid data to gain a systems-level understanding of a process.</p><p>The Japan Consortium for Glycobiology and Glycotechnology Database (JCGGDB) is a database of glycoscience data accumulated in Japan. It includes an integrated search function for eight databases accessible from JCGGDB. A high-quality resource of JCGGDB is the provision of all experimentally verified glyco-genes in humans, with each record annotated with literature references and provided with a graphical view of substrate specificity. Much of the data has been accumulated from the experimental data obtained at the National Institute of Advanced Industrial Science and Technology, which houses JCGGDB. These include MS data, lectin affinity data, glycoprotein data, and glyco-gene information. In KEGG GLYCAN, various tools have been added to interface glycomics data with genomic/transcriptomics information with a composite structure map summarizing the structures in the database and their relationships. Moreover, glyco-related genes (e.g., glycosyltransferases and GBPs) have been organized in KEGG BRITE in terms of the KEGG orthology (KO). Thus, genomic and functional analysis of glyco-related genes and glycan structures can be performed using the KEGG resources.</p><p>UniCarbKB also aims to integrate complementary -omics data to provide a knowledgebase for glycomics information. UniCarbKB provides contextual information for the glycan structures in the database as attached to proteins, and where known, shows the connection between a specific glycan structure and the attached proteins as annotated in the proteomics knowledgebase UniProtKB. The coverage and content of UniCarbKB depends on efforts to curate current literature that contain characterized glycan structures and their sites of attachment to proteins, with supporting data on experimental conditions and biological sources.</p><p>This integration of complex molecular data from all types of analytical techniques and interactions is in its infancy, but is essential for the continued progress of glycobiological research.</p></div><div id="Ch52_s7"><h2 id="_Ch52_s7_">FUTURE PERSPECTIVES FOR GLYCOINFORMATICS DEVELOPMENT</h2><div id="Ch52_s7a"><h3>Computational Needs</h3><div id="Ch52_s7a1"><h4>Development of Web Services (RESTful)</h4><p>Web services are a common technology that enables programmers to write computer programs that can access data via the Web. Data providers write application programming interfaces (APIs) to allow other programmers to access their data. The advantage of Web services is that it provides more flexibility to bioinformaticians, in particular, to access data. Web services can also be used within other webpages to automatically obtain search results (e.g., for a particular query sent via the Web service). Data providers can also control the data that can be accessed and the kinds of queries that can be made by providing web service APIs, thus assuring some level of security in terms of database access.</p></div><div id="Ch52_s7a2"><h4>Semantic Web and Ontologies</h4><p>In contrast to Web services, the Semantic Web is a new technology that provides a framework for making data available directly on the Internet, provided with semantics, such that inferences can be made automatically based on the data. For example, a researcher often refers to various publications to come up with a new hypothesis to test. Using the Semantic Web, the data in the publications would be formatted in such a way (using predefined vocabulary, or ontologies) such that the meaning behind the data is preserved in a computable form. Because a common vocabulary, or ontology, would be used across different publications in different websites (i.e., journals), the terminology used to encapsulate the semantics is preserved. With such data available on the Semantic Web, machine learning technologies allow computers to make inferences based on the data available, just as a researcher would think of new hypotheses.</p><p>The Semantic Web is based on the RDF that defines data as <i>triples,</i> consisting of a subject, predicate, and object, such that semantics can be incorporated into the data. Thus, it is important that ontologies are defined and standardized such that data providers use common terminology to define their RDF data. The BioPortal is a major resource of ontologies for the life sciences, within which GlycoRDF, GlycO, and other glycomics ontologies are centrally stored. As more ontologies are developed by the community, and as more life science database developers use RDF, the Semantic Web will become a powerful tool to integrate the glycosciences with other life science fields, including genomics, proteomics, and lipidomics.</p></div></div><div id="Ch52_s7b"><h3>Functional Connections</h3><div id="Ch52_s7b1"><h4>Glycobiology As a Part of Systems Biology</h4><p>Systems biology involves the development, simulation, and analysis of biological systems (including whole-body and environmental systems) at the molecular and cellular levels. As research on glycan biosynthetic pathway simulation progresses, its integration with protein-level systems biology will allow for a better understanding of glycosylation processes and interactions with GBPs.</p><p>The current coordinated trend toward RDF-based data integration is already shaping future developments of glycoscience databases. It will help bridge the gap between glycomics and other -omics that have already adopted RDF ontologies but that are still very much DNA sequence-centered. Indeed, 30 years after the advent of sequencing technology, DNA sequences, along with their links to other data types (gene expression, protein structure, etc.), remain the most prominent entities in molecular biology databases and repositories. Scientists gather sequence-centered information in the course of elucidating a cellular process or a pathological behavior, simply because a gene/protein sequence is usually the common element shared across -omics domains. The problem here is that glycans are only linked to the gene via their biosynthetic enzymes and substrates. The advancement of glycoscience as a discipline depends on expanding the integration of data describing glycoproteins, glycolipids, glycosaminoglycans, lipopolysaccharides, and the genome-coded enzymatic machinery that generates or breaks down these glycans, together with the ever increasing information about the interactions of these glycoconjugates with other components of the cell.</p></div><div id="Ch52_s7b2"><h4>Linking Glycan Structures with Function</h4><p>It is the ultimate goal of glycoscience research to be able to link glycan structures with their function. Although it is still difficult to completely identify fully defined glycan structures in a high-throughput manner, various hypotheses regarding the relationships between the specific structure of a glycan and its biological functions have been developed. One hypothesis maintains that the structural features characteristic of a group of glycans, rather than of a single structure, are required for biological function. This hypothesis is probable but is unlikely to be valid in all cases, as many discrete glycans are known to have quite specific functions, and changing a single monosaccharide or glycosidic conformation can greatly affect their capacity to realize their functions. Thus, additional work is required to accumulate as much of the experimental glycomics data as possible into standardized formats, such that comprehensive, integrated analyses can be performed using bioinformatics technologies.</p></div><div id="Ch52_s7b3"><h4>Collaboration in Glycoinformatics</h4><p>The future of current endeavors in glyco-related informatics lies in the consolidation of international consortia. The small size of the glycoscience community has prompted several cooperative initiatives across all continents for representing and collecting glycomics data (as described above). To favor interactions between these complementary initiatives, the international Glycome Informatics Consortium (GLIC) has been founded in 2015 to provide and maintain a centralized software resource enabling cooperative database and tool development. Also in 2015, a Glycomics section was established on the SIB ExPASy proteomics resource portal, and glycoprotein entries in UniProtKB were linked to glycan structural information where known in UniCarbKB. In addition, the National Institutes of Health, USA as part of the Common Fund Glycoscience Program is now focused on creating new methodologies and resources to study glycans that include the development of data integration and analysis tools.</p></div></div></div><div id="Ch52_s8"><h2 id="_Ch52_s8_">LONG-RANGE PERSPECTIVE</h2><p>These international efforts are affirmation that the importance of bioinformatics resources for glycoscience is finally being recognized, such that the role of glycans may be more easily understood and accessed by the broader research community. But it is clear that there is a long way to go before the entire community can have routine access to what aficionados of nucleic acid and protein biology currently take for granted: reliable, well-curated, user-friendly, cross-referenced databases that are permanently and safely housed in major long-term government-funded central servers. Achievement of this goal will be critical to bringing the study of glycans into the mainstream of evolutionary, molecular and cellular biology, and its applications to medicine, materials science, and other fields that benefit humankind.</p></div><div id="ack49"><h2 id="_ack49_">ACKNOWLEDGMENTS</h2><p>The authors acknowledge contributions to previous versions of this chapter by Ram Sasisekharan and appreciate helpful comments and suggestions from Shadi Toghi Eshghi, Morten Thaysen-Andersen, and David B. Nix.</p></div><div id="rl52"><h2 id="_rl52_">FURTHER READING</h2><ul class="simple-list"><li class="half_rhythm"><p><div class="bk_ref" id="CH52C1">Doubet S, Bock K, Smith D, Darvill A, Albersheim P. 1989. The Complex Carbohydrate Structure Database. Trends Biochem Sci
|
|
14:
|
|
475–477. [<a href="https://pubmed.ncbi.nlm.nih.gov/2623761" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 2623761</span></a>]</div></p></li><li class="half_rhythm"><p><div class="bk_ref" id="CH52C2">Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M. 2006. KEGG as a glycome informatics resource. Glycobiology
|
|
16:
|
|
63–70. [<a href="https://pubmed.ncbi.nlm.nih.gov/16014746" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 16014746</span></a>]</div></p></li><li class="half_rhythm"><p><div class="bk_ref" id="CH52C3">Ranzinger R, Herget S, Wetter T, von der Lieth CW. 2008. GlycomeDB—Integration of open-access carbohydrate structure databases. BMC Bioinformatics
|
|
9:
|
|
384. [<a href="/pmc/articles/PMC2567997/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC2567997</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/18803830" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 18803830</span></a>]</div></p></li><li class="half_rhythm"><p><div class="bk_ref" id="CH52C4">Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH. 2014. UniCarbKB: Building a knowledge platform for glycoproteomics. Nucleic Acids Res
|
|
42 (Database issue): D215–D221. [<a href="/pmc/articles/PMC3964942/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC3964942</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/24234447" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 24234447</span></a>]</div></p></li><li class="half_rhythm"><p><div class="bk_ref" id="CH52C5">Varki A, Cummings RD, Aebi M, Packer NH, Seeberger PH, Esko JD, Stanley P, Hart G, Darvill A, Kinoshita T, et al.
|
|
2015. Symbol nomenclature for graphical representations of glycans. Glycobiology
|
|
25:
|
|
1323–1334. [<a href="/pmc/articles/PMC4643639/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC4643639</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/26543186" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 26543186</span></a>]</div></p></li><li class="half_rhythm"><p><div class="bk_ref" id="CH52C7">Aoki-Kinoshita K, Agravat S, Aoki NP, Arpinar S, Cummings RD, Fujita A, Fujita N, Hart GM, Haslam SM, Kawasaki T, et al.
|
|
2017. GlyTouCan 1.0—The international glycan structure repository. Nucleic Acids Res
|
|
44:
|
|
D1237–D1242. [<a href="/pmc/articles/PMC4702779/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC4702779</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/26476458" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 26476458</span></a>]</div></p></li><li class="half_rhythm"><p><div class="bk_ref" id="CH52C6">Hu H, Khatri K, Zaia J. 2017. Algorithms and design strategies towards automated glycoproteomics analysis. J Mass Spectrom Rev doi: 10.1002/mas.21487. [<a href="/pmc/articles/PMC4931994/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC4931994</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/26728195" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 26728195</span></a>] [<a href="http://dx.crossref.org/10.1002/mas.21487" ref="pagearea=cite-ref&targetsite=external&targetcat=link&targettype=uri">CrossRef</a>]</div></p></li></ul></div><div id="bk_toc_contnr"></div></div></div><div class="fm-sec"><h2 id="_NBK453097_pubdet_">Publication Details</h2><h3>Author Information and Affiliations</h3><p class="contrib-group"><h4>Authors</h4><span itemprop="author">Matthew P. Campbell</span>, <span itemprop="author">Kiyoko F. Aoki-Kinoshita</span>, <span itemprop="author">Frederique Lisacek</span>, <span itemprop="author">William S. York</span>, and <span itemprop="author">Nicolle H. Packer</span>.</p><h3>Publication History</h3><p class="small">Published online: 2017.</p><h3>Copyright</h3><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright</a> 2015-2017 by The Consortium of Glycobiology Editors, La Jolla, California. All rights reserved.<p class="small">PDF files are not available for download.</p></div></div><h3>Publisher</h3><p><a href="http://www.cshlpress.com/default.tpl?action=full&cart=12210755385880789&--eqskudatarq=666" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">Cold Spring Harbor Laboratory Press</a>, Cold Spring Harbor (NY)</p><h3>NLM Citation</h3><p>Campbell MP, Aoki-Kinoshita KF, Lisacek F, et al. Glycoinformatics. 2017. In: Varki A, Cummings RD, Esko JD, et al., editors. Essentials of Glycobiology [Internet]. 3rd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2015-2017. Chapter 52.<span class="bk_cite_avail"></span> doi: 10.1101/glycobiology.3e.052</p></div><div class="small-screen-prev"><a href="/books/n/glyco3/ch51/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M75,30 c-80,60 -80,0 0,60 c-30,-60 -30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Prev</text></svg></a></div><div class="small-screen-next"><a href="/books/n/glyco3/ch53/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M25,30c80,60 80,0 0,60 c30,-60 30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Next</text></svg></a></div></article><article data-type="fig" id="figobch52f1"><div id="ch52.f1" class="figure bk_fig"><div class="graphic"><img data-src="/books/NBK453097/bin/ch52f01.jpg" alt="FIGURE 52.1.. The critical role of glycomics in systems biology." /></div><h3><span class="label">FIGURE 52.1.</span></h3><div class="caption"><p>The critical role of glycomics in systems biology. Glycan structures have no template from which to be predicted, are regulated by cellular metabolism and glyco-enzyme expression, and modify both proteins and lipids. Glycomics thus requires the tools of genomics, proteomics, lipidomics, and metabolomics to be integrated by bioinformatics.</p></div><p><a href="/books/NBK453097/bin/ch52f01.pptx">Download Teaching Slide</a><span class="small"> (PPTX, 1.8M)</span></p></div></article><article data-type="table-wrap" id="figobCH52TB1"><div id="CH52TB1" class="table"><h3><span class="label">TABLE 52.1.</span></h3><div class="caption"><p>List of available glycoscience-related informatics</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK453097/table/CH52TB1/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__CH52TB1_lrgtbl__"><table class="no_bottom_margin"><colgroup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:xi="http://www.w3.org/2001/XInclude" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:pmc="http://www.pubmedcentral.gov/pmc" xmlns:xlink="http://www.w3.org/1999/xlink" span="1"><col align="left" span="1" /><col align="left" span="1" /><col align="left" span="1" /></colgroup><thead><tr><th id="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Database</th><th id="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Description</th><th id="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">URL</th></tr></thead><tbody><tr><td headers="hd_h_CH52TB1_1_1_1_1 hd_h_CH52TB1_1_1_1_2 hd_h_CH52TB1_1_1_1_3" colspan="3" rowspan="1" style="vertical-align:top;">
|
|
<b>Structure databases</b>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">KEGG GLYCAN</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan structures, references to reactions and pathways, glyco-gene information</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.genome.jp/kegg/glycan" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.genome.jp/kegg/glycan</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">CFG</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan structures, MS profile, GlycanArray data, glyco-gene expression data</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.functionalglycomics.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.functionalglycomics.org</a>
|
|
<a href="http://www.glycome-db.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glycome-db.org</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GLYCOSCIENCES.de</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan structures, 3D structures, NMR data, software tools</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycosciences.de" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glycosciences.de</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">MonosaccharideDB</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">repertoire of monosaccharides</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.monosaccharidedb.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.monosaccharidedb.org</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">UniCarbKB</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">literature-based curated glycan structures, glycoprotein site/global information</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.unicarbkb.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.unicarbkb.org</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">JCGGDB</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan structures, glyco-gene information, glycomics-related protocols, cross references</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://jcggdb.jp/index_en.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://jcggdb<wbr style="display:inline-block"></wbr>​.jp/index_en.html</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">CSDB</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">bacterial, fungi, and plant glycan structures, NMR data</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://csdb.glycoscience.ru/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://csdb<wbr style="display:inline-block"></wbr>​.glycoscience.ru/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlyTouCan</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan structure registry</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glytoucan.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glytoucan.org</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycoEpitope</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan epitopes</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycoepitope.jp" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glycoepitope.jp</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycoPedia</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">information on glycobiology</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycopedia.eu/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glycopedia.eu/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1 hd_h_CH52TB1_1_1_1_2 hd_h_CH52TB1_1_1_1_3" colspan="3" rowspan="1" style="vertical-align:top;">
|
|
<b>Ontologies and Guidelines</b>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycO ontology</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">curated glycan structures</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://bioportal.bioontology.org/ontologies/3169" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://bioportal<wbr style="display:inline-block"></wbr>​.bioontology<wbr style="display:inline-block"></wbr>​.org/ontologies/3169</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycoRDF</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan structures, experimental data, biological source</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycoinfo.orf" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glycoinfo.orf</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">MIRAGE</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">experimental reporting guidelines</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.beilstein-institut.de/en/projects/mirage" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.beilstein-institut<wbr style="display:inline-block"></wbr>​.de/en/projects/mirage</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1 hd_h_CH52TB1_1_1_1_2 hd_h_CH52TB1_1_1_1_3" colspan="3" rowspan="1" style="vertical-align:top;">
|
|
<b>Analytical Tools</b>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">UniCarb-DB</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan structures, LC/MS-MS, HPLC data</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.unicarb-db.expasy.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.unicarb-db.expasy.org</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycoMob</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">ion mobility collisional cross sections</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycomob.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glycomob.org</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycoBase and autoGU</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan structures, HPLC profiles</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://glycobase.nibrt.ie" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://glycobase<wbr style="display:inline-block"></wbr>​.nibrt.ie</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycoWorkBench</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan MS/MS data analysis</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://code.google.com/archive/p/glycoworkbench/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://code<wbr style="display:inline-block"></wbr>​.google.com<wbr style="display:inline-block"></wbr>​/archive/p/glycoworkbench/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">Sweet-Heart</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycoproteomic data analysis</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://sweet-heart.glycoproteomics.proteome.bc.sinica.edu.tw" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://sweet-heart<wbr style="display:inline-block"></wbr>​.glycoproteomics<wbr style="display:inline-block"></wbr>​.proteome.bc.sinica.edu.tw</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GRITS Toolbox</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">integrated glycoanalytics</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.grits-toolbox.org/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.grits-toolbox.org/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycoDigest</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">exoglycosidase digest prediction</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycoproteome.expasy.org/glycodiaest/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http:<wbr style="display:inline-block"></wbr>​//glycoproteome<wbr style="display:inline-block"></wbr>​.expasy.org/glycodigest/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycoMod</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">composition of glycan</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://web.expasy.org/glycomod" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://web<wbr style="display:inline-block"></wbr>​.expasy.org/glycomod</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">RINGS</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">software tools</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.rings.t.soka.ac.jp" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.rings.t.soka.ac.jp</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">Glycomics@ExPASy</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">software tools</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.expacy.org/glycomics" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.expasy.org/glycomics</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1 hd_h_CH52TB1_1_1_1_2 hd_h_CH52TB1_1_1_1_3" colspan="3" rowspan="1" style="vertical-align:top;">
|
|
<b>Glyco-Enzymes</b>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">CAZy</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">carbohydrate-active enzymes</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.cazy.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.cazy.org</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">BRENDA</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">enzyme classification database</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.brenda-enzymes.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.brenda-enzymes.org</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1 hd_h_CH52TB1_1_1_1_2 hd_h_CH52TB1_1_1_1_3" colspan="3" rowspan="1" style="vertical-align:top;">
|
|
<b>Glycan Binding</b>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">RINGS</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">software tools</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.rings.t.soka.ac.jp" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.rings.t.soka.ac.jp</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlycoPattern</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">glycan array and glycan-binding protein analysis</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://glycopattern.emory.edu/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://glycopattern<wbr style="display:inline-block"></wbr>​.emory.edu/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">SugarBind</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">curated information on pathogen–glycan binding</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://sugarbind.expasy.org/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://sugarbind<wbr style="display:inline-block"></wbr>​.expasy.org/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">MatrixDB</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">extracellular matrix interaction database</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://matrixdb.univ-lyon1.fr/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://matrixdb<wbr style="display:inline-block"></wbr>​.univ-lyon1.fr/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1 hd_h_CH52TB1_1_1_1_2 hd_h_CH52TB1_1_1_1_3" colspan="3" rowspan="1" style="vertical-align:top;">
|
|
<b>3D/Modeling/NMR</b>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlyCAM</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">collection of tools for 3D modeling and simulation of carbohydrate structures</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycam.org" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glycam.org</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">Sweet-II</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">3D modeling</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycosciences.de/modeling/sweet2/doc/index.php" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glycosciences<wbr style="display:inline-block"></wbr>​.de/modeling/sweet2/doc/index.php</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">Glyco3D</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">3D structure database</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glyco3d.cermav.cnrs.fr" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glyco3d.cermav.cnrs.fr</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">PDB-Care</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">PDB carbohydrate validation</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycosciences.de/tools/pdb-care/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.glycosciences<wbr style="display:inline-block"></wbr>​.de/tools/pdb-care/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">GlyVicinity</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">statistical analysis</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.glycosciences.de/tools/glyvicinity/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">www<wbr style="display:inline-block"></wbr>​.glycosciences.de/tools/glyvicinity/</a>
|
|
</td></tr><tr><td headers="hd_h_CH52TB1_1_1_1_1" rowspan="1" colspan="1" style="vertical-align:top;">CASPER</td><td headers="hd_h_CH52TB1_1_1_1_2" rowspan="1" colspan="1" style="vertical-align:top;">determination of oligosaccharide and polysaccharide structures</td><td headers="hd_h_CH52TB1_1_1_1_3" rowspan="1" colspan="1" style="vertical-align:top;">
|
|
<a href="http://www.casper.organ.su.se/casper" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www<wbr style="display:inline-block"></wbr>​.casper.organ.su.se/casper</a>
|
|
</td></tr></tbody></table></div><div class="tblwrap-foot"><div><dl class="temp-labeled-list small"><dl class="bkr_refwrap"><dt></dt><dd><div><p class="no_margin">MS, mass spectrometry; 3D, three-dimensional; NMR, nuclear magnetic resonance; LC, liquid chromatography; HPLC, high-performance liquid chromatography; PDB, Protein Data Bank.</p></div></dd></dl></dl></div></div></div></article></div><div id="jr-scripts"><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/libs.min.js"> </script><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.min.js"> </script></div></div>
|
|
|
|
|
|
|
|
|
|
<!-- Book content -->
|
|
|
|
<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js"> </script>
|
|
|
|
|
|
<!-- CE8B5AF87C7FFCB1_0191SID /projects/books/PBooks@9.11 portal105 v4.1.r689238 Tue, Oct 22 2024 16:10:51 -->
|
|
<span id="portal-csrf-token" style="display:none" data-token="CE8B5AF87C7FFCB1_0191SID"></span>
|
|
|
|
<script type="text/javascript" src="//static.pubmed.gov/portal/portal3rc.fcgi/4216699/js/3968615.js" snapshot="books"></script></body>
|
|
</html>
|