CINXE.COM

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Challenges : EMDataResource</title> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">  <script async src="https://www.googletagmanager.com/gtag/js?id=G-0N32KDVZDG"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-0N32KDVZDG'); </script> <meta property="og:title" content="EMDataResource" /> <meta property="og:type" content="website" /> <meta property="og:url" content="https://www.emdataresource.org" /> <meta property="og:image" content="/images/EMDataResource-logo-small.png" /> <link rel="shortcut icon" href="/favicon.ico"> <link href="/css/bootstrap4.1.3.min.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> <link href="/css/em-styles-cutdown.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> <link href="/css/navbar.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> <script src="/js/jquery-3.3.1.min.js" type="text/javascript"></script> <script src="/js/popper1.12.9.min.js" type="text/javascript"></script> <script src="/js/bootstrap4.1.3.min.js" type="text/javascript"></script> <script type="text/javascript" src="/js/bootstrap3-typeahead.min.js"></script> </head> <body> <div class="container"> <div class="card" style="border: none; margin-bottom: 0px;" > <div class="card-header clearfix" style="background-color: #CCC;"> <div class="float-left"><b><span id="siteid"></span></b></div> <script> var sitebanner="" if (location.hostname.search("test") != -1) {sitebanner = "PRE-PRODUCTION STAGING SITE"; } if (location.hostname.search("159.51") != -1) {sitebanner = "PRE-PRODUCTION STAGING SITE"; } else if (location.hostname.search("dev") != -1) {sitebanner = "DEVELOPMENT SITE"; } else if (location.hostname.search("beta") != -1) {sitebanner = "BETA TESTING SITE"; } else if (location.hostname.search("4.80") != -1) {sitebanner = "REVIEW SITE"; } document.getElementById("siteid").innerHTML = sitebanner; </script> <div class="float-right"><span id="update_date">2025-02-12</span> : <span id="map_entries">42644</span> EMDB map entries, <span id="coordinate_entries">24982 PDB coordinate entries <a href="https://go.rutgers.edu/zcuqsog5" target="_blank">RCSB PDB</a> | <a href="https://go.rutgers.edu/paqlf60v" target="_blank" >PDBe</a> </span>  </div> </div> <div class="card-body" style="padding: 2px 15px;" > <div class="float-left"><a href="/index.html"> <img src="/images/EMDataResource-logo-small.png" alt="EMDataResource.org" height="78" style="margin-right: 25px;" /> </a></div> </div> <nav class="navbar navbar-expand-lg navbar-dark"> <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div class="collapse navbar-collapse" id="navbarSupportedContent"> <ul class="nav navbar-nav mr-auto"> <li class="nav-item"> <a class="nav-link" href="/index.html">Home</a></li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> About</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/mission.html">Mission</a> <a class="dropdown-item" href="/team.html">Team</a> <a class="dropdown-item" href="/dictionaries.html">Dictionaries</a> <a class="dropdown-item" href="/conventions.html">Conventions</a> <a class="dropdown-item" href="/validation.html">Validation</a> <a class="dropdown-item" href="/project_publications.html">Publications</a> <a class="dropdown-item" href="/funding.html">Funding</a> </div> </li> <li class="nav-item"><a class="nav-link" href="/deposit.html">Deposit</a></li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Search</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/emdlist=all">EMDR Search</a> <a class="dropdown-item" href="/coronavirus_search.html">CoV Enhanced Search</a> <a class="dropdown-item" href="/solrfacet.html">EMDR Search Term Facet Tool</a> <a class="dropdown-item" href="/searchnonrel.html">Search Proc/Hold/Obs/Wdrn Entries</a> <a class="dropdown-item" href="/search.html">All EMDB Search Options</a> </div> </li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Tools</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/statistics.html">Statistics</a> <a class="dropdown-item" href="https://ptp.emdataresource.org">RNA Virtual Torsion Analysis</a> <a class="dropdown-item" href="/emsoftware.html">EM Software List</a> <a class="dropdown-item" href="/emtestdata.html">3DEM Test Data</a> <a class="dropdown-item" href="/emdbaccess.html">EMDB Access</a> </div> </li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Archive</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown">  <a class="dropdown-item" href="/challenges/index.html">EMDR Challenges</a> <a class="dropdown-item" href="/workshops.html">Workshops</a> <a class="dropdown-item" href="/emdbac.html">Advisory Committee</a> </div> </li> <li class="nav-item"><a class="nav-link" href="/allnews.html">News</a></li> <li class="nav-item"><a class="nav-link" href="/externallinks.html">Links</a></li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Help</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/contactus.html">Contact Us</a> <a class="dropdown-item" href="/faq.html">FAQ</a> </div> </li> </ul> <form class="form-inline my-2 my-lg-0"> <input id="homequery" class="form-control typeahead mr-sm-2" data-sho-hint-on-focus="true" data-provide="typeahead" autocomplete="off" data-autoselect="false" type="search" placeholder="Search EMDB" aria-label="Search EMDB"> <button id="btnSearch" class="btn btn-secondary my-2 my-sm-0" type="submit" style="background-color: #CCC;" ><img src="/images/search_icon.svg" alt="search" /></button> </form> </div> </nav> <div class="card-body"> <h2>EMDataResource Challenges</h2> <p>This page serves as a summary archive of the EMDataResource team's interactions with the 3DEM community to establish data validation methods for Cryo-EM structures. Following recommendations of the <a href="/vtf">EM Validation Task Force</a> (<a href="http://dx.doi.org/10.1016/j.str.2011.12.014" target="_blank">Henderson et al 2012</a>), EMDR hosted and organized the Challenge activities listed below. Links are provided to publications and special journal issues as well as <a href="https://zenodo.org/communities/3dcryoemchallenges/" target="_blank">Zenodo-hosted Challenge data archives.</a></p>  <figure class="figure"> <img src="/challenges/docs/2017_CryoEM_Workshop-6-2.jpg" class="figure-img img-fluid rounded" alt="Participants in the 2017 CryoEM Structure Joint Challenges Workshop."> <figcaption class="figure-caption">October 6-8, 2017 CryoEM Structure Joint Challenges Workshop. SLAC Campus, Stanford University, California.</figcaption> </figure> <br/> <div id="accordion"> <div class="card"><div class="card-header"><a class="card-link" data-toggle="collapse" href="#collapse2021">2021 Ligand Model Challenge</a></div> <div id="collapse2021" class="collapse" data-parent='#accordion'><div class="card-body"> <ul> <li>Summary Publication (peer reviewed): <a href="https://pubmed.ncbi.nlm.nih.gov/38918604/">Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. </a>Nat Methods 21, 1340-1348 (2024). <a class="badge badge-light" href="https://doi.org/10.1038/s41592-024-02321-7" target="_blank">doi</a></li> <li>Summary Publication (preprint version): <a href="https://pubmed.ncbi.nlm.nih.gov/38343795/">Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.</a> </li> <li>Archived Data: <a href= "https://zenodo.org/records/10551958" target="_blank">2021 EMDataResource Ligand Model Challenge Dataset</a></li> <li>Interactive Data Tables/Plots: <a href="https://model-compare.emdataresource.org/2021/cgi-bin/index.cgi" target="_blank">2021 Model Challenge</a></li> <li>Wrap-Up Workshop: <a href="https://rutgers.box.com/s/a2ak9xc2bjpsxombw1v3kw0zuxlpqbdm">Agenda and Documents</a></li> </ul> </div></div></div> <div class="card"><div class="card-header"><a class="card-link" data-toggle="collapse" href="#collapse2019">2019 Model Metrics Challenge</a></div> <div id="collapse2019" class="collapse" data-parent='#accordion'><div class="card-body"> <ul> <li>Summary Publication: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33542514">Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge</a> Nat Methods. 2021 Feb;18(2):156-164. Epub 2021 Feb 4. <a class="badge badge-light" href="https://doi.org/10.1038/s41592-020-01051-w" target="_blank">doi</a></li> <li>Archived Data: <a href="https://zenodo.org/records/4148789" target="_blank">2019 EMDataResource Model Metrics Challenge Dataset</a></li> <li>Interactive Data Tables/Plots: <a href="https://model-compare.emdataresource.org/2019/cgi-bin/index.cgi" target="_blank">2019 Model Challenge</a></li> <li>Wrap-Up Workshop: <a href="https://rutgers.app.box.com/s/svi5ha7l7hgvfw1l3a58ydjx0soe0wtn">Agenda and Documents</a></li> </ul> </div></div></div> <div class="card"><div class="card-header"><a class="card-link" data-toggle="collapse" href="#collapse2016">2016 Map & Model Challenges</a></div> <div id="collapse2016" class="collapse" data-parent='#accordion'><div class="card-body"> <ul> <li>Journal Special Issue: <a href="https://www.sciencedirect.com/journal/journal-of-structural-biology/special-issue/108PXM64R4D">CryoEM Challenges Journal of Structural Biology (2018--19 articles)</a> </li> <li>Editorial Overview: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30321594" target="_blank"> Comparing cryo-EM structures.</a> J Struct Biol. 2018 Oct 13. pii: S1047-8477(18)30277-6. <a class="badge badge-light" href="https://doi.org/10.1016/j.jsb.2018.10.004" target="_blank">doi</a> </li> <li>Data Processing: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30263915"> Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge.</a> Data Brief. 2018 Sep 8;20:1629-1638. <a class="badge badge-light" href="https://doi.org/10.1016/j.dib.2018.08.214" target="_blank">doi</a> </li> <li>Archived Data: <a href="https://zenodo.org/records/1165999" target="_blank">CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge</a></li> <li>Archived Data: <a href="https://zenodo.org/records/1185426" target="_blank">CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge</a></li> <li>Interactive Data Tables/Plots: <a href="https://model-compare.emdataresource.org/2016/cgi-bin/index.cgi" target="_blank">2016 Model Challenge</a></li> <li>Wrap-Up Workshop: <a href="https://rutgers.box.com/s/bggqqpez7v2m7rwqjdqzof5tyhm2zdlc">Agenda and Documents</a></li> </ul> </div></div></div> <div class="card"><div class="card-header"><a class="card-link" data-toggle="collapse" href="#collapse2010">2010 Model Challenge</a></div> <div id="collapse2010" class="collapse" data-parent='#accordion'><div class="card-body"> <ul> <li>Journal Special Issue: <a href="https://onlinelibrary.wiley.com/toc/10970282/2012/97/9" target="_blank">Biopolymers Vol 97, Issue 9: The 2010 Cryo-EM Modeling Challenge (9 articles)</a></li> <li>Editorial Overview: <a href="http://www.ncbi.nlm.nih.gov/pubmed/22696402" target="_blank">The 2010 cryo-EM modeling challenge.</a> Biopolymers. 2012 Sep;97(9):651-4. <a class="badge badge-light" href="https://doi.org/10.1002/bip.22081" target="_blank">doi</a> </li> </ul> </div></div></div> </div> </div> <footer class="page-footer"> <div class="container-fluid"> <div class="row" style="color:#666; background-color: #E4E4E4; padding-top: 18px; padding-bottom: 3px;"> <div class="col-sm-2" style="padding-top: 10px; padding-bottom: 10px;"> <a href="https://cryoem.slac.stanford.edu" target="_blank"> <img src="/images/ncmi-logo.png" alt="Stanford-CryoEM" height="35px"/></a> </div> <div class="col-sm-2" style="padding-top: 10px; padding-bottom: 10px;"> <a href="https://www.rcsb.org" target="_blank"> <img src="/images/rcsb-pdb-logo.png" alt="PDB" height="35px"/></a> </div> <div class="col-sm-2" style="padding-top: 10px; padding-bottom: 10px;"> <a href="https://www.ebi.ac.uk/emdb/" target="_blank"> <img src="/images/EMDB_logo_2017.png" alt="EMDB" height="35px"/></a> </div> <div class="col-sm-6"> <div class="float-right text-right"> <p style="margin-bottom: 0px;"> Prior Support from<br />National Institutes of Health<br />National Institute of General Medical Sciences</p> </div> </div> </div> <div class="row" style="color:#FFF; background-color: #666; padding-top: 3px; padding-bottom: 8px;"> <div class="col-sm-2">   </div> <div class="col-sm-10"> <div class="small float-right text-right" style="margin-top: 8px;" > © 2007-2025 EMDataResource</div> </div> </div> </div> </footer> </div> </div>  <script> $.get("/js/auto.json", function(data){ $("#homequery").typeahead({ source: data, items: 8, minLength: 1, delay: 60, autoSelect: true, }); },'json'); $('#btnSearch').on('click', function () { var url; var searchInput = $('#homequery').val(); //minimum of 3 characters var regex0 = new RegExp ( "(.){3,}" ); var results0 = regex0.exec( searchInput ); if (results0 !== null) { //test for an EMDB id with or without "EMD-" prefix var regex1 = new RegExp ( "^[eE][mM][dD]-[0-9]{4,}$" ); var regex2 = new RegExp ( "^[0-9]{4,}$" ); //pure number 4+ digits var results1 = regex1.exec( searchInput ); var results2 = regex2.exec( searchInput ); if (results1 !== null) { url = "/EMD-" + searchInput.slice(4); window.open(url); } else if (results2 !== null) { url = "/EMD-" + searchInput; window.open(url); } else { url = "/?emdlist=" + searchInput; window.open(url); } } }); </script> </body> </html>