1<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 2<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> 3<head> 4<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> 5<meta name="viewport" content="width=device-width, initial-scale=1.0"> 6<title>About NAKB</title> 7<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> 8 9<!-- Global site tag (gtag.js) - Google Analytics -->
vendor: 64 bytes, lines 9-10
9 10<script async src="https://www.googletagmanager.com/gtag/js?id=
10G-0K2RSNBJTZ
vendor: 12 bytes, line 10
10"></script>
11<script> 12
vendor: 133 bytes, lines 12-15
12window.dataLayer = window.dataLayer || []; 13 function gtag(){dataLayer.push(arguments);} 14 gtag('js', new Date()); 15 gtag('config', '
15G-0K2RSNBJTZ
vendor: 5 bytes, line 15
15');
16</script>
16 17 18<meta property="og:title" content="Nucleic Acid Knowledge Base" /> 19<meta property="og:type" content="website" /> 20<meta property="og:url" content="https://nakb.org" /> 21<meta property="og:image" content="/images/nakb-logo-500px.png" /> 22 23 24<link rel="icon" href="/favicon.ico" type="image/x-icon"/> 25<link rel="shortcut icon" href="/favicon.ico" type="image/x-icon"/> 26 27<link href="/css/bootstrap4.1.3.min.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> 28<link href="/css/extra-styles.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> 29
30<script src="/js/jquery-3.3.1.min.js" type="text/javascript"></script>
vendor: 1 bytes, line 30
30
31<script src="/js/popper1.12.9.min.js" type="text/javascript"></script>
vendor: 1 bytes, line 31
31
32<script src="/js/bootstrap4.1.3.min.js" type="text/javascript"></script>
32 33
34<script src="/js/share.js" type="text/javascript"></script>
vendor: 1 bytes, line 34
34
35<script src="/js/NAKBprotdict.js" type="text/javascript"></script>
vendor: 1 bytes, line 35
35
36<script src="/js/NAKBnadict.js" type="text/javascript"></script>
vendor: 1 bytes, line 36
36
37<script src="/js/NAKBliganddict.js" type="text/javascript"></script>
vendor: 1 bytes, line 37
37
38<script src="/js/PPCdict.js" type="text/javascript"></script>
38 39
40<script type="text/javascript" src="/js/bootstrap3-typeahead.min.js"></script>
40 41 42
43<script> 44var sitebanner=""; 45if (location.hostname.search("dev") != -1) {sitebanner = "DEVELOPMENT SITE"; } 46//else if (location.hostname.search("beta") != -1) {sitebanner = "BETA TESTING SITE"; } 47</script>
47 48
49<script> $(function () { $('[data-toggle="tooltip"]').tooltip({ trigger : 'hover' }) }) </script>
49 50 51 52</head> 53 <body> 54<div class="container-fluid"> 55<div class="row" style="background-color: #CCC;"> 56<div class="col-md-6" style="margin-top: 8px; margin-bottom: 8px;"> <b><span id="siteid"></span></b></div> 57
58<script> document.getElementById("siteid").innerHTML = sitebanner;</script>
58 59 60<div class="col-md-6" style="margin-top: 8px; margin-bottom: 8px;"> <div class="float-right"><span id='update_date'>2026-09-30</span> : 22510 3D structures containing nucleic acids | RNAEQ <a target='_blank' href='http://rna.bgsu.edu/rna3dhub/nrlist/release/4.59/all'>v4.59all</a> </div> 61 </div> 62</div> 63</div> <!--end row--> 64 65<div class="row" > 66<div class="col-lg-2" style="margin-top: 4px; margin-bottom: 0px;"> 67<a href="/"><img src="/images/nakb-logo.svg" alt="nakb.org" height="65" style="margin-left: 10px; margin-right: 10px;" /></a></div> 68<div class="col-lg-4" style="margin-top: 30px; margin-bottom: 10px;"><center><!--a class='badge badge-external' href="/annotations.html"><i>June 2023: New NA, Protein Annotation Trees</i></a--></center></div> 69 70<div class="col-lg-6" style="margin-top: 24px; "> <div class="float-right"> 71 <form class="form-inline"> 72 <div class="input-group mb-3"> 73 <a href="/nakblist=all" target="_blank" id="searchall" class="btn btn-primary" ><b>Full Search</b></a> 74 <input id="homequery" class="form-control typeahead" data-show-hint-on-focus="true" 75 data-provide="typeahead" autocomplete="off" data-autoselect="false" 76 type="search" placeholder="Quick Search: enter PDB/NDB id, author or keyword" size="48" aria-label="Search NAKB"> 77 <button id="btnSearch" class="btn btn-secondary" type="submit" 78 style="background-color: #CCC; margin-right: 10px;" ><img src="/images/search_icon.svg" alt="search" /></button> 79 </div></form><br/> 80<!--h3>Portal for 3D structural information about Nucleic Acids </h3--></div> 81</div> 82</div> 83</div> 84 85 86<nav class="navbar navbar-expand-lg navbar-dark"> 87 <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation"> 88 <span class="navbar-toggler-icon"></span> 89 </button> 90 91 92 <div class="collapse navbar-collapse" id="navbarSupportedContent"> 93 <ul class="nav navbar-nav mr-auto"> 94 95 <li class="nav-item"><a class="nav-link" href="/">Home</a></li> 96 97 98 <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" 99 role="button" aria-haspopup="true" aria-expanded="false">Tools</a> 100 101 <div class="dropdown-menu" aria-labelledby="navbarDropdown"> 102 <a class="dropdown-item" href="/nakblist=all" >Full Search</a> 103 <a class="dropdown-item" href="/annotations.html">Explore Annotations: Tree Views</a> 104 <a class="dropdown-item" href="/searchterms.html">Explore Annotations: Table Views</a> 105 <a class="dropdown-item" href="/statistics.html" >Custom Charts</a> 106 <a class="dropdown-item" href="/modifiednt.html" >Modified Nucleotide Browser</a> 107 <a class="dropdown-item" href="/natools.html">External Resources</a> 108 </div> 109 </li> 110 111 112 <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" 113 role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Education</a> 114 115 <div class="dropdown-menu" aria-labelledby="navbarDropdown"> 116 <a class="dropdown-item" href="/basics/intro.html">Introduction to Nucleic Acids</a> 117 <a class="dropdown-item" href="/ndbmodule/bp-catalog/">RNA Basepair Catalog</a> 118 <a class="dropdown-item" href="/basics/pdb101.html">NA Molecules of the Month</a> 119 <a class="dropdown-item" href="/basics/rnaj.html"><i>RNA Journal</i> Cover Images</a> 120 <a class="dropdown-item" href="/ndbmodule/music/">DNA Music Atlas</a> 121 </div> </li> 122 123 <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" 124 role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Standards</a> 125 126 <div class="dropdown-menu" aria-labelledby="navbarDropdown"> 127 <a class="dropdown-item" href="/basics/valencegeometry.html">Valence Geometry <span style="color:red"><b>2026 Update!</b></span></a> 128 <a class="dropdown-item" href="/basics/nucleotides.html">Nucleotides</a> 129 <a class="dropdown-item" href="/basics/basepairs.html">Base Pairs</a> 130 </div> </li> 131 132 <li class="nav-item"><a class="nav-link" href="/download.html">Download</a></li> 133 134 <li class="nav-item"><a class="nav-link" href="/about.html">About</a></li> 135 136 </ul> 137 138 </div><!-- navbar header--> 139 </nav> 140 141 <div class="card-body"> 142 143<div class="row"> 144<div class="col-md-6"> 145<div class="card"> <div class="card-header"> <h3>NAKB Team</h3> </div> 146<div class="card-body"> 147<ul> 148<li><a href="https://sites.rutgers.edu/catherine-lawson" target="_blank">Catherine L Lawson</a>, Rutgers University</li> 149<li><a href="https://rutchem.rutgers.edu/people/emeritus-faculty/emeritus-faculty-member/120-berman-helen" target="_blank">Helen M Berman</a>, Rutgers University </li> 150<li>Brinda Vallat, Rutgers University </li> 151<li>Li Chen, Rutgers University </li> 152<li><a href="https://www.bgsu.edu/arts-and-sciences/mathematics-and-statistics/faculty-and-staff/craig-zirbel.html" target="_blank">Craig L Zirbel</a>, Bowling Green State University </li> 153<li><a href="https://www.bgsu.edu/arts-and-sciences/chemistry/faculty/neocles-b-leontis.html" target="_blank">Neocles B Leontis</a>, Bowling Green State University (deceased)</li> 154</ul> 155</div> 156</div> 157<div class="card"> <div class="card-header"> <h3>NDB Co-founders</h3> </div> 158<div class="card-body"> 159<ul> 160<li>Helen M Berman, Rutgers University </li> 161<li>Wilma K Olson, Rutgers University </li> 162<li>David Beveridge, Wesleyan University </li> 163</ul> 164</div> 165</div> 166<div class="card"> <div class="card-header"> <h3>About NAKB</h3> </div> 167<div class="card-body"> 168 169<p>The Nucleic Acid Knowledge Base (NAKB), modern successor to the Nucleic Acid Database (NDB) Project, archives and distributes structural information about nucleic acids. Development and implementation of NAKB has been funded by the National Institutes of Health R01 GM085328. NDB has been funded by National Science Foundation and the Department of Energy in the past. </p> 170<p>NAKB's home is the <a href="https://iqb.rutgers.edu" target="_blank">Institute for Quantitative Biomedicine</a>, Rutgers University, 174 Frelinghuysen Rd, Piscataway, NJ USA, 08854-8076</p> 171</div> 172</div> 173<div class="card"> <div class="card-header"> <h3>How to cite</h3> </div> 174<div class="card-body"> 175 <p> Researchers who use NAKB should cite: <ul> 176<li> Lawson CL, Berman HM, Vallat B, Chen L, Zirbel C (2024) <i>The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.</i> Nucleic Acids Research 52, D245-D254. <a class='badge badge-external' href="https://doi.org/10.1093/nar/gkad957" target="_blank">DOI</a></li></ul></p> 177 <p> Researchers who use the NDB should cite: <ul> 178<li> Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B (1992)<i> 179The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. </i> Biophys. J. 63, 751-759. <a class='badge badge-external' href="https://doi.org/10.1016/S0006-3495(92)81649-1" target="_blank">DOI</a> </li> 180<li>Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM (2014) <i>The Nucleic Acid Database: new features and capabilities. </i>Nucleic Acids Res 42, D114-22. <a class='badge badge-external' href="https://doi.org/10.1093/nar/gkt980" target="_blank">DOI</a> </li> 181</ul> </p> <p> The history of NDB and plan for NAKB are described here: <ul><li>Berman HM, Lawson CL, Schneider B (2022) <i>Developing Community Resources for Nucleic Acid Structures. </i>Life 12, 540. <a class='badge badge-external' href="https://doi.org/10.3390/life12040540" target="_blank">DOI</a> 182</li></ul> </p> 183</div> 184</div> 185 186</div> 187<div class="col-md-6"> 188 189<div class="card"> <div class="card-header"> <h3>Contact us</h3> </div> 190<div class="card-body"> 191 192 <p>Please send questions, comments, suggestions about NAKB to <a href="mailto:[email protected]">[email protected]</a>.</p> 193 194</div> 195</div> 196 197<div class="card"> <div class="card-header"> <h3>Data Resources</h3> </div> 198<div class="card-body"> 199<p>NAKB is currently updated weekly on Thursdays, ~noon US ET (timing may change in future). Current update info is shown in the banner at the top of every page.</p> 200<div id="resourcetable"></div> 201<i>*Beginning October 8, 2025, Rfam-PDB chain mappings are obtained from both Rfam (updated semi-annually) and BGSU RNA 3D Hub (updated weekly).</i> 202</div> 203</div> 204 205<div class="card"> <div class="card-header"> <h3>Software</h3> </div> 206<div class="card-body"> 207 208<table class='table table-sm' style='width:100%'> 209<tr><th>NAKB Feature(s)</th> <th></th><th>Software</th></tr> 210<tr><td>2D fold diagrams</a></td><td></td><td><a class='badge badge-internal' href="https://github.com/rcsb/RNAView" target="_blank">RNAview</a> v.2.0</td></tr> 211<tr><td>NA parameter tables, annotations</td><td></td><td><a class='badge badge-external' href="https://x3dna.org" target="_blank">X3DNA-DSSR</a> v.2.4</td></tr> 212<tr><td>
212NA and Protein Sequence Clusters</a></td><td></td><td><a class='badge badge-external' href="https://github.com/weizhongli/cdhit/wiki/" target="_blank">CD-HIT, CD-HIT-EST</a>v.4.8.1</td></tr> 213<tr><td>template-based 2D fold viewer</a></td><td></td><td><a class='badge badge-external' href="https://github.com/r2dt-bio/R2DT" target="_blank">R2DT</a>v.2.0</td></tr> 214<tr><td>3D visualization</a></td><td></td><td><a class='badge badge-external' href="https://github.com/molstar/rcsb-molstar" target="_blank">Mol*</a></td></tr> 215</table> 216 217 218 219 220 221</div> 222</div> 223 224 225 226</div> 227</div> 228 229 <br class="clearfloat" /> 230 <!-- end card-body --></div> 231 <footer class="page-footer"> 232 <div class="container-fluid"> 233 234<div class="row" style="color:#FFF; background-color: #3FAFEF; background-image: linear-gradient(to right, #2E3192, #3FAFEF); padding-top: 3px; padding-bottom: 8px;"> 235<div class="col-sm-2"> 236</div> 237<div class="col-sm-10"> 238<div class="small float-right text-right" style="margin-top: 8px;" > 239Supported by NIH National Institute of General Medical Sciences, © 2022-2026 NAKB</div> 240</div> 241</div> 242</div> 243</footer> 244<!--/div--><!-- end of panel started in header.html --> 245</div> <!--end of container started in header.html--> 246
247<script> 248 249$.get("/js/nakbauto.json", function(data){ $("#homequery").typeahead({ 250 source: data, 251 items: 8, 252 minLength: 1, 253 delay: 60, 254 //autoSelect: true, 255 autoSelect: false, 256 }); 257 },'json'); 258 259$('#btnSearch').on('click', function () { 260 var url; 261 var searchInput = $('#homequery').val(); 262 //minimum of 3 characters 263 var regex0 = new RegExp ( "(.){3,}" ); 264 var results0 = regex0.exec( searchInput ); 265 if (results0 !== null) { 266 var results1 = ndbidregex.exec( searchInput ); 267 var results2 = pdbidregex.exec( searchInput ); 268 var results3 = extpdbidregex.exec( searchInput ); 269 if (results1 !== null) { url = "/atlas=" + searchInput.toUpperCase(); window.open(url); } 270 else if (results2 !== null) { url = "/atlas=" + searchInput.toUpperCase(); window.open(url); } 271 else if (results3 !== null) { url = "/atlas=" + searchInput; window.open(url); } 272 else { url = "/?nakblist=" + searchInput; window.open(url); } 273} 274}); 275 276</script>
276 277 278 279 280</body> 281</html> 282
283<script> 284//START 285const dataresources = [ 286{ type: "internal", resource: "NAKB Annotations", rlink: "/download.html", freq: "weekly", version: "banner date"}, 287{ type: "external", resource: "RCSB PDB (API)", rlink: "rcsb.org", freq: "weekly", version: "banner date"}, 288{ type: "external", resource: "Representative RNA Structure Sets", rlink: "http://rna.bgsu.edu/rna3dhub/nrlist/", freq: "weekly", version: "banner version"}, 289{ type: "external", resource: "DNATCO", rlink: "https://dnatco.datmos.org/", freq: "weekly", version: ""}, 290{ type: "external", resource: "DNAproDB", rlink: "https://dnaprodb.usc.edu/", freq: "weekly", version: ""}, 291{ type: "external", resource: "G4DSSR", rlink: "http://g4.x3dna.org/DSSR-G4DB.html", freq: "weekly", version: ""}, 292{ type: "external", resource: "ONQUADRO", rlink: "https://onquadro.cs.put.poznan.pl/home", freq: "", version: "2022-07-17"}, 293{ type: "external", resource: "RNACentral", rlink: "https://rnacentral.org/", freq: "semiannual", version: "v26 2025-10-08"}, 294{ type: "external", resource: "Rfam", rlink: "https://rfam.org/", freq: "semiannual*", version: "v15 2024-09-16"}, 295{ type: "external", resource: "3D FootPrint", rlink: "https://3dfootprint.eead.csic.es/", freq: "semiannual", version: "2024-09-14"}, 296{ type: "external", resource: "PANTHER Protein Classes", rlink: "https://pantherdb.org/", freq: "annual", version: "v19.0 2024-06-20"}, 297{ type: "external", resource: "RNAscape", rlink: "https://rnascape.usc.edu/", freq: "", version: ""}, 298{ type: "external", resource: "Modomics", rlink: "https://genesilico.pl/modomics/", freq: "", version: ""} 299] ; 300//END 301 302var txt = "<table class='table table-sm' style='width:100%'>" + "<tr><th>Resource</th> <th>Update Frequency</th><th>Version</th></tr>"; 303$.each(dataresources, function(i, item) { 304txt += "<tr><td><a class='badge badge-" + item["type"] + "' href='" + item["rlink"] + "' target='_blank'>" + item["resource"] + "</a></td><td>" + item["freq"] + "</td><td>" + item["version"] + "</td></tr>"; 305} ); 306txt += '</table>'; 307 308$('#resourcetable').append(txt); 309</script>
vendor: 1 bytes, line 309
309
Line numbers count LF bytes from the start of the resource, as the search results do. Vendor segments are library code the classifier recognised; they are stored but not indexed. Bytes are shown as Latin1 characters, one per byte.