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>EM Software : 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>  <link href="/css/dataTables.bootstrap4.min.css" rel="stylesheet"/> <link href="/css/pagination.css" rel="stylesheet"/> <script src="/js/jquery.dataTables.min.js"></script> <script src="/js/dataTables.bootstrap4.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">2025-02-19</span> : <span id="map_entries">42759</span> EMDB map entries, <span id="coordinate_entries">25065 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">  <div class="row"> <div class="container"> <h2>EM software</h2> Below is a list of software programs for generation, fitting, and analysis of 3D maps from electron microscopy images. See also: <a href="http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy" target="_blank">EM software wiki page</a>. Please send corrections/additions to <a href="mailto:help@emdataresource.org">help@emdataresource.org</a>.<br /><br /> <table class="table table-striped table-sm" id="sort" style="width:100%"> <thead> <tr> <th scope="col">Program</th> <th scope="col">Type</th> <th scope="col">Reference</th> </tr> </thead> <tbody>  <tr> <td><a href="https://focus.c-cina.unibas.ch/" target="_blank"><img src="./images/elink.svg" width="20px" alt="Link" /></a> Focus (successor to 2dx)</td> <td>General Package</td> <td><a href="https://doi.org/10.1016/j.jsb.2017.03.007" target="_blank">Biyani et al 2017</a></td> </tr> <tr> <td><a href="http://www.ual.es/~jjfdez/SW/embfactor.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> EMBFACTOR</td> <td>Bfactor correction</td> <td><a href="https://doi.org/10.1016/j.jsb.2008.05.010" target="_blank">Fernandez et al 2008</a></td> </tr> <tr> <td><a href="http://www.cnb.csic.es/~jjfernandez/tomoalign" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> TomoAlign</td> <td>Image alignment, Tomography</td> <td><a href="https://doi.org/10.1016/j.jsb.2018.02.001" target="_blank">Fernandez et al 2018</a></td> </tr> <tr> <td><a href="http://nramm.nysbc.org/downloads/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> ACE/ACE2</td> <td>CTF correction</td> <td><a href="https://doi.org/10.1016/j.ultramic.2005.02.004" target="_blank">Mallick et al 2005</a></td> </tr> <tr> <td><a href="http://grigoriefflab.janelia.org/ctf" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> ctffind/ctftilt</td> <td>CTF correction</td> <td><a href="http://dx.doi.org/10.1016/j.jsb.2015.08.008" target="_blank">Rohou & Grigorieff 2015</a></td> </tr> <tr> <td><a href="http://www.ual.es/~jjfdez/software" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> EMCTF/TOMOCTF</td> <td>CTF correction</td> <td><a href="http://dx.doi.org/10.1016/j.ultramic.2006.02.004" target="_blank">Fernandez & Crowther 2006</a></td> </tr> <tr> <td><a href="http://leginon.org/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Leginon</td> <td>data acquisition</td> <td><a href="https://doi.org/10.1016/j.jsb.2005.03.010" target="_blank">Suloway et al 2005</a></td> </tr> <tr> <td><a href="http://www.msg.ucsf.edu/em/EMNEW2/tomography_page.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> UCSF Tomography</td> <td>data acquisition, tomography</td> <td><a href="https://doi.org/10.1016/j.jsb.2004.02.005" target="_blank">Zheng et al 2004</a></td> </tr> <tr> <td><a href="http://www.ual.es/~jjfdez/software/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> TOMOAND/TOMOBFLOW</td> <td>denoising</td> <td><a href="https://doi.org/10.1016/j.jsb.2003.09.010" target="_blank">Fernandez & Li 2003</a></td> </tr> <tr> <td><a href="http://lsbr.niams.nih.gov/bsoft/bsoft.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Bsoft</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1002/pro.3293" target="_blank">Heymann 2018</a></td> </tr> <tr> <td><a href="https://cistem.org/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> cisTEM</td> <td>reconstruction</td> <td><a href="https://doi.org/10.7554/eLife.35383" target="_blank">Grant et al 2018</a></td> </tr> <td><a href="http://cryosparc.com" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> CryoSPARC</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1038/nmeth.4169" target="_blank">Punjani et al 2017</a></td> </tr> <tr> <td><a href="http://blake.bcm.edu/emanwiki/EMAN2" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> EMAN/EMAN2</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1016/j.jsb.2018.09.002" target="_blank">Bell et al 2018</a></td> </tr> <tr> <td><a href="http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Eos</td> <td>reconstruction</td> <td></td> </tr> <tr> <td><a href="http://www.imagescience.de/imagic.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> IMAGIC</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1006/jsbi.1996.0004">van Heel et al 1996</a></td> </tr> <tr> <td><a href="http://www.iplt.org/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> IPLT</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1016/j.jsb.2013.02.017" target="_blank">Schenk et al 2013</a></td> </tr> <tr> <td><a href="http://www.ccpem.ac.uk/download.php" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> CCP-EM</td> <td>reconstruction, model refinement, validation</td> <td><a href="https://doi.org/10.1107/S2059798317007859" target="_blank">Burnley et al 2017</a></td> </tr> <tr> <td><a href="http://simplecryoem.com/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Simple</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1002/pro.3266" target="_blank">Reboul et al 2018</a></td> </tr> <tr> <td><a href="http://sparx-em.org" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Sparx</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1016/j.jsb.2011.12.020" target="_blank">Behrmann et al 2012</a></td> </tr> <tr> <td><a href="http://spider.wadsworth.org" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Spider</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1107/97809553602060000874" target="_blank">Leith et al 2012</a></td> </tr> <tr> <td><a href="http://emg.nysbc.org/redmine/projects/suprim" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Suprim</td> <td>reconstruction</td> <td></td> </tr> <tr> <td><a href="http://sphire.mpg.de/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> SPHIRE</td> <td>reconstruction</td> <td><a href="https://doi.org/10.3791/55448" target="_blank">Moriya et al 2017</a></td> </tr> <tr> <td><a href="http://xmipp.cnb.csic.es/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Xmipp</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1016/j.jsb.2013.09.015" target="_blank">de la Rosa-Trev铆 et al 2013</a></td> </tr> <tr> <td><a href="mailto:egelman@virginia.edu" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> IHRSR</td> <td>helical</td> <td><a href="https://doi.org/10.1016/S0076-6879(10)82006-3" target="_blank">Egelman 2010</a></td> </tr> <tr> <td><a href="http://emg.nysbc.org/redmine/projects/phoelix" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Phoelix</td> <td>helical</td> <td><a href="https://doi.org/10.1006/jsbi.1996.0018" target="_blank">Carragher et al 1996</a></td> </tr> <tr> <td><a href="http://structure.m.u-tokyo.ac.jp/English/software/Ruby-Helix-Page/ruby-helix.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Ruby-Helix</td> <td>helical</td> <td><a href="https://doi.org/10.1016/j.jsb.2006.07.015" target="_blank">Metlagel et al 2007</a></td> </tr> <tr> <td><a href="http://www.sachse.embl.de/emspring" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Spring</td> <td>helical</td> <td><a href="https://doi.org/10.1016/j.jsb.2013.11.003" target="_blank">Desfosses et al 2014</a></td> </tr> <tr> <td><a href="https://bakerlab.ucsd.edu/wikis/software/start.php?id=auto3dem:home" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> AUTO3DEM</td> <td>icosahedral</td> <td><a href="https://doi.org/10.1016/j.jsb.2006.08.007" target="_blank">Yan et al 2007</a></td> </tr>  <tr> <td><a href="https://www.imagescience.de/em2em.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> em2em</td> <td>map conversion</td> <td><a href="https://doi.org/10.1006/jsbi.1996.0004">van Heel et al 1996</a></td> </tr> <tr> <td><a href="http://chaconlab.org/methods/fitting/adpem" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> ADP_EM</td> <td>modelling</td>  <td><a href="https://doi.org/10.1093/bioinformatics/btl625" target="_blank">Garzon et al 2007</a></td> </tr> <tr> <td><a href="http://www.cgl.ucsf.edu/chimera/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> UCSF Chimera</td> <td>modelling, visualization</td> <td><a href="https://doi.org/10.1002/jcc.20084" target="_blank">Petterson et al 2004</a></td> </tr> <tr> <td><a href="http://www.cgl.ucsf.edu/chimerax/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> ChimeraX</td> <td>modelling, visualization</td> <td><a href="https://doi.org/10.1002/pro.3235" target="_blank">Goddard et al 2018</a></td> </tr> <tr> <td><a href="http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> COOT</td> <td>modelling, visualization</td> <td><a href="https://doi.org/10.1107/S1399004714021683" target="_blank">Brown et al 2015</a></td> </tr> <tr> <td><a href="https://simtk.org/home/direx/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> DireX</td> <td>modelling</td> <td><a href="https://doi.org/10.1002/bip.22046" target="_blank">Wang & Schroeder 2012</a></td> </tr> <tr> <td><a href="https://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/emfit.php" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> EMfit</td> <td>modelling</td> <td><a href="https://doi.org/10.1006/jsbi.2002.4435" target="_blank">Rossmann et al 2001</a></td> </tr> <tr> <td><a href="http://topf-group.ismb.lon.ac.uk/flex-em/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Flex-EM</td> <td>modelling</td> <td><a href="https://doi.org/10.1016/j.ymeth.2016.03.007" target="_blank">Joseph et al 2016</a></td> </tr> <tr> <td><a href="http://gorgon.wustl.edu/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Gorgon</td> <td>modelling</td> <td><a href="https://doi.org/10.1002/bip.22065" target="_blank">Baker et al 2012</a></td> </tr> <tr> <td><a href="http://chaconlab.org/hybrid4EM/imodfit" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> iMODFIT</td> <td>modelling</td> <td><a href="https://doi.org/10.1016/j.jsb.2013.08.010" target="_blank">Lop茅z-Banco & Chacon 2013</a></td> </tr> <tr> <td><a href="http://www.ks.uiuc.edu/Research/vmd/plugins/mdff/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> MDFF</td> <td>modelling</td> <td><a href="https://doi.org/10.1016/j.ymeth.2009.04.005" target="_blank">Trabuco et al 2009</a></td> </tr <tr> <td><a href="http://mmtsb.org/software/nmff.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> NMFF</td> <td>modelling</td> <td><a href="https://doi.org/10.1016/j.jmb.2004.01.048" target="_blank">Tama et al 2004</a></td> </tr> <tr> <td><a href="http://www.sciences.univ-nantes.fr/elnemo/NORMA/WWW/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> NORMA</td> <td>modelling</td> <td><a href="https://doi.org/10.1107/S090744490602244X" target="_blank">Suhre et al 2006</a></td> </tr> <tr> <td><a href="https://www.phenix-online.org" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Phenix</td> <td>model refinement, validation</td> <td><a href="https://doi.org/10.1107/S2059798318006551" target="_blank">Afonine et al 2018</a></td> </tr> <tr> <td><a href="http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> REFMAC</td> <td>modelling</td> <td><a href="https://doi.org/10.1107/S1399004714021683" target="_blank">Brown et al 2015</a></td> </tr> <tr> <td><a href="http://dimaiolab.ipd.uw.edu/software/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Rosetta for cryoEM</td> <td>modelling</td> <td><a href="https://doi.org/10.7554/eLife.17219" target="_blank">Wang et al 2016</a></td> </tr> <tr> <td><a href="http://situs.biomachina.org/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Situs</td> <td>modelling</td> <td><a href="https://doi.org/10.1186/s12900-018-0089-0" target="_blank">Kovacs et al 2018</a></td> </tr> <tr> <td><a href="http://tempy.ismb.lon.ac.uk/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> TEMPy</td> <td>modelling, model validation</td> <td><a href="https://doi.org/10.1107/S1600576715010092" target="_blank">Farabella et al 2015</a></td> </tr>  <tr> <td><a href="http://www.ks.uiuc.edu/Research/vmd/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> VMD</td> <td>modelling, visualization</td> <td></td> </tr> <td><a href="http://fraserlab.com/2015/02/18/EMringer/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> EMRinger</td> <td>model validation</td> <td><a href="https://doi.org/10.1038/nmeth.3541" target="_blank">Barad et al 2015</a></td> </tr> <tr> <td><a href="http://molprobity.biochem.duke.edu/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Molprobity</td> <td>model validation</td> <td><a href="https://doi.org/10.1002/pro.3330" target="_blank">Williams et al 2018</a></td> </tr> <tr> <td><a href="https://sites.google.com/site/maofuliao/samviewer" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> SamViewer</td> <td>particle picking</td> <td></td> </tr> <tr> <td><a href="http://grigoriefflab.janelia.org/signature" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Signature</td> <td>particle picking</td> <td><a href="https://doi.org/10.1016/j.jsb.2006.06.001" target="_blank">Chen & Grigorieff 2007</a></td> </tr> <tr> <td><a href="http://www.imagescience.de/fsc.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> FSC</td> <td>resolution estimation</td> <td><a href="https://doi.org/10.1006/jsbi.1996.0004">van Heel et al 1996</a></td> </tr> <tr> <td><a href="http://grigoriefflab.janelia.org/rmeasure" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> rmeasure</td> <td>resolution estimation</td> <td><a href="https://doi.org/10.1016/j.jsb.2006.08.003" target="_blank">Sousa & Grigorieff 2007</a></td> </tr> <tr> <td><a href="http://grigoriefflab.janelia.org/frealign" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Frealign</td> <td>reconstruction</td> <td><a href="http://dx.doi.org/10.1016/j.jsb.2013.07.005" target="_blank">Lyumkis et al 2013</a></td> </tr> <tr> <td><a href="http://cores.utah.edu/pft3dr-package/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> PFT3DR</td> <td>reconstruction</td> <td></td> </tr> <tr> <td><a href="http://www2.mrc-lmb.cam.ac.uk/relion" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> RELION</td> <td>reconstruction</td> <td><a href="https://doi.org/10.1016/j.jsb.2012.09.006" target="_blank">Scheres 2012</a></td> </tr> <tr> <td><a href="https://c-cina.unibas.ch/tools/soft/dynamo/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Dynamo</td> <td>tomography</td> <td><a href="https://doi.org/10.1016/j.jsb.2011.12.017" target="_blank">Castano-Diez et al 2012</a></td> </tr> <tr> <td><a href="http://em3d.stanford.edu/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> EM3D</td> <td>tomography</td> <td><a href="https://doi.org/10.1016/j.str.2004.07.022" target="_blank" >Ress et al 2004</a></td> </tr>  <tr> <td><a href="http://bio3d.colorado.edu/imod/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> IMOD</td> <td>tomography</td> <td><a href="https://doi.org/10.1016/j.jsb.2016.07.011" target="_blank">Mastronarde & Held 2017</a></td> </tr> <tr> <td><a href="http://www.electrontomography.org/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> protomo</td> <td>tomography</td> <td><a href="https://doi.org/10.1016/j.ultramic.2005.07.007" target="_blank">Winkler & Taylor 2006</a></td> </tr> <tr> <td><a href="http://bio3d.colorado.edu/SerialEM/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> SerialEM</td> <td>data acquisition, tomography</td> <td><a href="https://doi.org/10.1016/j.jsb.2005.07.007" target="_blank">Mastronarde 2005</a></td> </tr> <tr> <td><a href="http://www.biochem.mpg.de/tom/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> TOM</td> <td>tomography</td> <td><a href="https://doi.org/10.1016/j.jsb.2004.10.006" target="_blank">Nickell et al 2005</a></td> </tr> <tr> <td><a href="https://www.fei.com/software/amira-avizo/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Amira-Avizo</td> <td>visualization</td> <td><a href="https://www.sciencedirect.com/science/article/pii/B978012387582250040X" target="_blank">Stalling et al 2005 </a>| <a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.129.6785&rep=rep1&type=pdf" target="_blank"> (pdf)</a></td> </tr> <tr> <td><a href="http://www.ccp4.ac.uk/MG/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> CCP4mg</td> <td>visualization</td> <td><a href="https://doi.org/10.1107/S0907444911007281" target="_blank">McNicholas et al 2011</a></td> </tr> <tr> <td><a href="http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/river_programs/rivem.php" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> RIVEM</td> <td>visualization</td> <td><a href="https://doi.org/10.1016/j.jsb.2006.10.013" target="_blank">Xiao and Rossmann 2007</a></td> </tr> <tr> <td><a href="http://appion.org/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Appion</td> <td>workflow</td> <td><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775544/" target="_blank">Lander et al 2009</a></td> </tr> <tr> <td><a href="http://scipion.i2pc.es/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Scipion</td> <td>workflow</td> <td><a href="https://doi.org/10.1016/j.jsb.2016.04.010" target="_blank">de la Rosa-Trevin 2016</a></td> </tr> <tr> <td><a href="http://msg.ucsf.edu/em/software/motioncor2.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> motioncor2</td> <td>movie frame alignment</td> <td><a href="http://dx.doi.org/10.1038/nmeth.4193" target="_blank">Zheng et al 2017</a></td> </tr> <tr> <td><a href="https://www.mrc-lmb.cam.ac.uk/kzhang/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Gautomatch</td> <td>particle picking</td> <td></td> </tr> <tr> <td><a href="https://www.mrc-lmb.cam.ac.uk/kzhang/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Gctf</td> <td>CTF correction</td> <td><a href="https://doi.org/10.1016/j.jsb.2015.11.003" target="_blank">Zhang 2016</a></td> </tr> <tr> <td><a href="http://resmap.sourceforge.net/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> ResMap</td> <td>Local Resolution Estimation</td> <td><a href="http://dx.doi.org/10.1038/nmeth.2727" target="_blank">Kucukelbir et al 2014</a></td> </tr> <tr> <td><a href="http://grigoriefflab.janelia.org/unblur" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Unblur/Summovie</td> <td>movie frame alignment</td> <td><a href="http://dx.doi.org/10.7554/eLife.06980" target="_blank">Grant & Grigorieff 2015</a></td> </tr> <tr> <td><a href="http://proteinformatics.charite.de/ngl-tools/fragfit/start.php" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> FragFit</td> <td>modelling server</td> <td><a href="https://doi.org/10.1093/nar/gky424" target="_blank">Tiemann et al 2018</a></td> </tr> <tr> <td><a href="http://milou.science.uu.nl/cgi/services/POWERFIT/powerfit/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Powerfit</td> <td>modelling server</td> <td><a href="https://doi.org/10.1016/j.jmb.2016.11.032" target="_blank">Zundert et al 2017</a></td> </tr> <tr> <td><a href="https://liao.hms.harvard.edu/samuel" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Samuel</td> <td>workflow scripts</td> <td></td> </tr> <tr> <td><a href="http://spr.math.princeton.edu/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> ASPIRE</td> <td>reconstruction</td> <td></td> </tr> <tr> <td><a href="https://github.com/PrincetonUniversity/APPLEpicker-python" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> APPLE-Picker</td> <td>particle picking</td> <td><a href="https://doi.org/10.1016/j.jsb.2018.08.012" target="_blank">Heimowitz et al 2018</a></td> </tr> <tr> <td><a href="https://github.com/tbepler/topaz" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Topaz</td> <td>particle picking</td> <td><a href="https://arxiv.org/abs/1803.08207" target="_blank">Bepler et al 2018</a></td> </tr> <tr> <td><a href="https://www.mpibpc.mpg.de/grubmueller/densityfitting" target="_blank" ><img src="./images/elink.svg" width="20px" al t="Link" /></a> CDMD</td> <td>modelling</td> <td><a href="https://elifesciences.org/articles/43542" target="_blank">Igaev et al 2019</a></td> </tr> <tr> <td><a href="http://sphire.mpg.de/wiki/doku.php?id=pipeline:window:cryolo" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> crYOLO</td> <td>particle picking</td> <td><a href="https://doi.org/10.1038/s42003-019-0437-z" target="_blank">Wagner et al 2019</a></td> </tr> <tr> <td><a href="https://www.mrc-lmb.cam.ac.uk/crusso/cryoEF/downloads.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> cryoEF</td> <td>analyse orientation distribution</td> <td><a href="https://doi.org/10.1038/s41467-017-00782-3" target="_blank">Naydenova 2017</a></td> </tr> <tr> <td><a href="https://www.jeolusa.com/PRODUCTS/Transmission-Electron-Microscopes-TEM/Analytical-Data-Optimization/Automated-Data-Acquisition-JADAS" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> JADAS</td> <td>data acquisition</td> <td><a href="" target="_blank"></a></td> </tr> <tr> <td><a href="https://github.com/StructuralBiology-ICLMedicine/lafter/blob/master/README.md" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> LAFTER</td> <td>local filtering, noise reduction</td> <td><a href="https://doi.org/10.1016/j.jsb.2018.11.011" target="_blank">Ramlaul et al 2019</a></td> </tr> <tr> <td><a href="https://github.com/gregdp/mapq" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> MAPQ/Q-score</td> <td>map-model fit per atom</td> <td><a href="https://doi.org/10.1038/s41592-020-0731-1" target="_blank">Pintilie et al 2020</a></td> </tr> <tr> <td><a href="https://isolde.cimr.cam.ac.uk/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Isolde</td> <td>model building in cryo-EM maps</td> <td><a href="https://doi.org/10.1107/s2059798318002425" target="_blank">Croll 2018</a></td> </tr> <tr> <td><a href="https://deeptracer.uw.edu/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> DeepTracer</td> <td>automated model building in cryo-EM maps</td> <td><a href="https://doi.org/10.1073/pnas.2017525118" target="_blank">Pfab et al. 2020</a></td> </tr> <tr> <td><a href="https://github.com/thorn-lab/haruspex" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> Haruspex</td> <td>neural network-based segmentation</td> <td><a href="https://doi.org/10.1002/anie.202000421" target="_blank">Mostosi et al. 2020</a></td> </tr> <tr> <td><a href="https://github.com/MaximilianBeckers/SPOC" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> SPoC</td> <td>False Discovery Rate FSC</td> <td><a href="https://doi.org/10.1016/j.jsb.2020.107579" target="_blank">Beckers and Sachse 2020</a></td> </tr> <tr> <td><a href="https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/emda/emda.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> EMDA</td> <td>EM Map/Model Manipulation tools</td> <td><a href="https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/index.html" target="_blank">MRC Murshudov Group</a></td> </tr> <tr> <td><a href="https://sbemimage.readthedocs.io/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> SBEMimage</td> <td>Data acquisition and monitoring, serial SEM</td> <td><a href="https://www.frontiersin.org/articles/10.3389/fncir.2018.00054/full" target="_blank">Titze et al 2018</a></td> </tr> <tr> <td><a href="http://cryodrgn.csail.mit.edu/" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> cryoDRGN</td> <td>reconstruction</td> <td><a href="https://www.nature.com/articles/s41592-020-01049-4" target="_blank">Zhong et al 2021</a></td> </tr> <tr> <td><a href="https://kiharalab.org/emsuites/daq.php" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> DAQ</td> <td>model validation</td> <td><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10024464/" target="_blank">Terashi et al 2022</a></td> </tr> <tr> <td><a href="https://kiharalab.org/emsuites/cryoread.php" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> CryoREAD</td> <td>modeling</td> <td><a href="https://doi.org/10.1038/s41592-023-02032-5" target="_blank">Wang Terashi Kihara 2023</a></td> </tr> <tr> <td><a href="https://teamtomo.org/resources/cryoet-software/emclarity/emclarity.html" target="_blank" ><img src="./images/elink.svg" width="20px" alt="Link" /></a> emClarity</td> <td>tomography</td> <td><a href="https://www.ncbi.nlm.nih.gov/pubmed?term=emClarity%3A%20software%20for%20high-resolution%20cryo-electron" target="_blank">Himes & Zhang 2018</a></td> </tr>  </tbody> </table> </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> <script> $(document).ready(function() { $('#sort').DataTable( { "lengthMenu": [[10, 25, 50, -1], [10, 25, 50, "All"]] } ); } ); </script> </body> </html>