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</style><table class="infobox vevent"><tbody><tr><th colspan="2" class="infobox-above summary">Chemistry Development Kit</th></tr><tr><td colspan="2" class="infobox-image logo"></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Programmer" title="Programmer">Original author(s)</a></th><td class="infobox-data"><a href="Christoph_Steinbeck" title="Christoph Steinbeck">Christoph Steinbeck</a>, Egon Willighagen, Dan Gezelter</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Programmer" title="Programmer">Developer(s)</a></th><td class="infobox-data">The CDK Project</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Initial release</th><td class="infobox-data">11 May 2001<span style="display:none"> (<span class="bday dtstart published updated">2001-05-11</span>)</span><sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup></td></tr><tr style="display: none;"><td colspan="2" class="infobox-full-data"></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_release_life_cycle" title="Software release life cycle">Stable release</a></th><td class="infobox-data">2.11<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> (March 29, 2025<span style="display:none"> (<span class="bday dtstart published updated">2025-03-29</span>)</span>) <span class=""><a class="external text external" href="https://en.wikipedia.org/w/index.php?title=Template:Latest_stable_software_release/Chemistry_Development_Kit&action=edit">[±]</a></span></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_release_life_cycle#Beta" title="Software release life cycle">Preview release</a></th><td class="infobox-data">2.2<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> (October 30, 2018<span style="display:none"> (<span class="bday dtstart published updated">2018-10-30</span>)</span>) <span class=""><a class="external text external" href="https://en.wikipedia.org/w/index.php?title=Template:Latest_preview_software_release/Chemistry_Development_Kit&action=edit">[±]</a></span></td></tr><tr style="display:none"><td colspan="2">

</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Repository_(version_control)" title="Repository (version control)">Repository</a></th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="https://github.com/cdk/cdk">github<wbr>.com<wbr>/cdk<wbr>/cdk</a></span></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Written in</th><td class="infobox-data"><a href="Java_(programming_language)" title="Java (programming language)">Java</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Operating_system" title="Operating system">Operating system</a></th><td class="infobox-data"><a href="Windows" class="mw-redirect" title="Windows">Windows</a>, <a href="Linux" title="Linux">Linux</a>, <a href="Unix" title="Unix">Unix</a>, <a href="MacOS" title="MacOS">macOS</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Computing_platform" title="Computing platform">Platform</a></th><td class="infobox-data"><a href="IA-32" title="IA-32">IA-32</a>, <a href="X86-64" title="X86-64">x86-64</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Available in</th><td class="infobox-data">English</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_categories#Categorization_approaches" title="Software categories">Type</a></th><td class="infobox-data"><a href="Chemoinformatics" class="mw-redirect" title="Chemoinformatics">Chemoinformatics</a>, <a href="Molecular_modelling" title="Molecular modelling">molecular modelling</a>, <a href="Bioinformatics" title="Bioinformatics">bioinformatics</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_license" title="Software license">License</a></th><td class="infobox-data"><a href="GNU_Lesser_General_Public_License" title="GNU Lesser General Public License">LGPL</a> 2.0</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Website</th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="http://cdk.github.io">cdk<wbr>.github<wbr>.io</a></span></td></tr></tbody></table>

<p>The <b>Chemistry Development Kit</b> (<b>CDK</b>) is computer <a href="Software" title="Software">software</a>, a <a href="Library_(computing)" title="Library (computing)">library</a> in the programming language <a href="Java_(programming_language)" title="Java (programming language)">Java</a>, for <a href="Chemoinformatics" class="mw-redirect" title="Chemoinformatics">chemoinformatics</a> and <a href="Bioinformatics" title="Bioinformatics">bioinformatics</a>.<sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> It is available for <a href="Microsoft_Windows" title="Microsoft Windows">Windows</a>, <a href="Linux" title="Linux">Linux</a>, <a href="Unix" title="Unix">Unix</a>, and <a href="MacOS" title="MacOS">macOS</a>. It is <a href="Free_and_open-source_software" title="Free and open-source software">free and open-source software</a> distributed under the <a href="GNU_Lesser_General_Public_License" title="GNU Lesser General Public License">GNU Lesser General Public License</a> (LGPL) 2.0.

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<div class="mw-heading mw-heading2"><h2 id="History">History</h2></div>

<p>The CDK was created by <a href="Christoph_Steinbeck" title="Christoph Steinbeck">Christoph Steinbeck</a>, Egon Willighagen and Dan Gezelter, then developers of <a href="Jmol" title="Jmol">Jmol</a> and <a href="JChemPaint" title="JChemPaint">JChemPaint</a>, to provide a common code base, on 27–29 September 2000 at the <a href="University_of_Notre_Dame" title="University of Notre Dame">University of Notre Dame</a>. The first source code release was made on 11 May 2011.<sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> Since then more than 100 people have contributed to the project,<sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> leading to a rich set of functions, as given below. Between 2004 and 2007, <i>CDK News</i> was the project's newsletter of which all articles are available from a public archive.<sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> Due to an unsteady rate of contributions, the newsletter was put on hold.

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<div class="infobox-journal-search" style="display:none;"></div><table class="infobox hproduct"><caption class="infobox-title" style="font-size:125%;"><i><span class="fn">CDK News</span></i></caption><tbody><tr><th scope="row" class="infobox-label">Language</th><td class="infobox-data" style="text-align:left;">English</td></tr><tr><th scope="row" class="infobox-label"><a href="Editor-in-chief" title="Editor-in-chief">Edited</a> by</th><td class="infobox-data" style="text-align:left;">Egon Willighagen, <a href="Christoph_Steinbeck" title="Christoph Steinbeck">Christoph Steinbeck</a></td></tr><tr><th colspan="2" class="infobox-header" style="background:#dfc;color:#000;">Publication details</th></tr><tr><th scope="row" class="infobox-label">History</th><td class="infobox-data" style="text-align:left;">2004-2007</td></tr><tr><th colspan="2" class="infobox-header" style="background:#dfc;color:#000;">Standard abbreviations<br><span class="infobox-journal-search " style="display:none;"><a rel="nofollow" class="external text" href="https://marcinwrochna.github.io/abbrevIso/?search=CDK_News">ISO 4</a> (<a rel="nofollow" class="external text" href="http://www.issn.org/services/online-services/access-to-the-ltwa/">alt</a>) <b>·</b> Bluebook (<a rel="nofollow" class="external text" href="https://westerncriminology.org/publications/bluebook-abbreviations/">alt</a>)<br><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/nlmcatalog?term=1614-7553%5BISSN%5D">NLM</a> (<a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/nlmcatalog?term=CDK+News%5BJournal%5D">alt</a>) <b>·</b> <a rel="nofollow" class="external text" href="https://mathscinet.ams.org/msnhtml/serials.pdf">MathSciNet</a> (<a rel="nofollow" class="external text" href="https://mathscinet.ams.org/mathscinet/search/journals.html?journalName=1614-7553&Submit=Search">alt</a> <span typeof="mw:File"><span title="Paid subscription required"></span></span>)</span></th></tr><tr><th scope="row" class="infobox-label"><a href="ISO_4" title="ISO 4">ISO 4</a></th><td class="infobox-data identifier" style="text-align:left;"><i>CDK News</i></td></tr><tr><th colspan="2" class="infobox-header" style="background:#dfc;color:#000;">Indexing<br><span class="infobox-journal-search " style="display:none;"><a rel="nofollow" class="external text" href="https://cassi.cas.org/searching.jsp?searchIn=issns&c=WIy460-R_DY&searchFor=1614-7553">CODEN</a> (<a rel="nofollow" class="external text" href="https://cassi.cas.org/searching.jsp?searchIn=issns&c=WIy460-R_DY&searchFor=">alt</a> <b>·</b> <a rel="nofollow" class="external text" href="https://cassi.cas.org/searching.jsp?searchIn=titles&c=WIy460-R_DY&searchFor=Chemistry+Development+Kit">alt2</a>) <b>·</b> <a rel="nofollow" class="external text" href="https://www.jstor.org/journals/16147553">JSTOR</a> (<a rel="nofollow" class="external text" href="https://www.jstor.org/action/showJournals?browseType=title">alt</a>) <b>·</b> <a rel="nofollow" class="external text" href="https://catalog.loc.gov/vwebv/search?searchArg1=1614-7553&argType1=all&searchCode1=KNUM&searchType=2">LCCN</a> (<a rel="nofollow" class="external text" href="https://catalog.loc.gov/vwebv/search?searchArg1=CDK+News&argType1=all&searchCode1=KTIL&searchType=2">alt</a>)<br><a rel="nofollow" class="external text" href="http://miar.ub.edu/issn/1614-7553">MIAR</a> <b>·</b> <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/nlmcatalog?term=1614-7553%5BISSN%5D">NLM</a> (<a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/nlmcatalog?term=CDK+News%5BJournal%5D">alt</a>) <b>·</b> <a rel="nofollow" class="external text" href="https://www.scopus.com/sources?sortField=citescore&sortDirection=desc&isHiddenField=false&field=issn&issn=1614-7553">Scopus</a> <b>·</b> <a rel="nofollow" class="external text" href="https://managementtools4.wlu.edu/LawJournals/">W&L</a></span></th></tr><tr><th scope="row" class="infobox-label"><span class="type"><a href="ISSN_(identifier)" class="mw-redirect" title="ISSN (identifier)">ISSN</a></span></th><td class="infobox-data" style="text-align:left;"><span class="value"><a rel="nofollow" class="external text" href="https://www.worldcat.org/search?fq=x0:jrnl&q=n2:1614-7553">1614-7553</a></span><br></td></tr></tbody></table>

<p>Later, unit testing, code quality checking, and <a href="Javadoc" title="Javadoc">Javadoc</a> validation was introduced. Rajarshi Guha developed a nightly build system, named Nightly, which is still operating at <a href="Uppsala_University" title="Uppsala University">Uppsala University</a>.<sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> In 2012, the project became a support of the <a href="InChI_Trust" class="mw-redirect" title="InChI Trust">InChI Trust</a>, to encourage continued development. The library uses JNI-InChI<sup id="cite_ref-10" class="reference"><a href="#cite_note-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> to generate <a href="International_Chemical_Identifier" title="International Chemical Identifier">International Chemical Identifiers</a> (InChIs).<sup id="cite_ref-11" class="reference"><a href="#cite_note-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup>

In April 2013, John Mayfield (né May) joined the ranks of release managers of the CDK, to handle the development branch.<sup id="cite_ref-12" class="reference"><a href="#cite_note-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup>

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<div class="mw-heading mw-heading2"><h2 id="Library">Library</h2></div>

<p>The CDK is a library, instead of a user program. However, it has been integrated into various environments to make its functions available. CDK is currently used in several applications, including the programming language <a href="R_(programming_language)" title="R (programming language)">R</a>,<sup id="cite_ref-13" class="reference"><a href="#cite_note-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> CDK-Taverna (a <a href="Taverna_workbench" class="mw-redirect" title="Taverna workbench">Taverna workbench</a> plugin),<sup id="cite_ref-14" class="reference"><a href="#cite_note-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> <a href="Bioclipse" title="Bioclipse">Bioclipse</a>, PaDEL,<sup id="cite_ref-15" class="reference"><a href="#cite_note-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> and Cinfony.<sup id="cite_ref-16" class="reference"><a href="#cite_note-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> Also, CDK extensions exist for Konstanz Information Miner (<a href="KNIME" title="KNIME">KNIME</a>)<sup id="cite_ref-17" class="reference"><a href="#cite_note-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> and for <a href="Microsoft_Excel" title="Microsoft Excel">Excel</a>, called LICSS (<a rel="nofollow" class="external autonumber" href="https://github.com/KevinLawson/excel-cdk">[1]</a>).<sup id="cite_ref-18" class="reference"><a href="#cite_note-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup>

</p><p>In 2008, bits of GPL-licensed code were removed from the library. While those code bits were independent from the main CDK library, and no copylefting was involved, to reduce confusions among users, the ChemoJava project was instantiated.<sup id="cite_ref-19" class="reference"><a href="#cite_note-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup>

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<div class="mw-heading mw-heading2"><h2 id="Major_features">Major features</h2></div>

<div class="mw-heading mw-heading3"><h3 id="Chemoinformatics">Chemoinformatics</h3></div>

<ul><li>2D <a href="Molecule_editor" title="Molecule editor">molecule editor</a> and generator</li>

<li>3D geometry generation</li>

<li>ring finding<sup id="cite_ref-20" class="reference"><a href="#cite_note-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-21" class="reference"><a href="#cite_note-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup></li>

<li><a href="Substructure_search" title="Substructure search">substructure search</a> using exact structures and <a href="Smiles_arbitrary_target_specification" class="mw-redirect" title="Smiles arbitrary target specification">Smiles arbitrary target specification</a> (SMARTS) like <a href="Query_language" title="Query language">query language</a></li>

<li><a href="QSAR" class="mw-redirect" title="QSAR">QSAR</a> descriptor calculation<sup id="cite_ref-22" class="reference"><a href="#cite_note-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup></li>

<li>fingerprint calculation, including the ECFP and FCFP fingerprints<sup id="cite_ref-23" class="reference"><a href="#cite_note-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup></li>

<li><a href="Force_field_(chemistry)" title="Force field (chemistry)">force field</a> calculations</li>

<li>many input-output <a href="Chemical_file_format" title="Chemical file format">chemical file formats</a>, including <a href="Simplified_molecular-input_line-entry_system" class="mw-redirect" title="Simplified molecular-input line-entry system">simplified molecular-input line-entry system</a> (SMILES), <a href="Chemical_Markup_Language" title="Chemical Markup Language">Chemical Markup Language</a> (CML), and <a href="Chemical_table_file" title="Chemical table file">chemical table file</a> (MDL)</li>

<li>structure generators<sup id="cite_ref-24" class="reference"><a href="#cite_note-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup></li>

<li><a href="International_Chemical_Identifier" title="International Chemical Identifier">International Chemical Identifier</a> support, via JNI-InChI</li></ul>

<div class="mw-heading mw-heading3"><h3 id="Bioinformatics">Bioinformatics</h3></div>

<ul><li>protein active site detection</li>

<li>cognate ligand detection<sup id="cite_ref-25" class="reference"><a href="#cite_note-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup></li>

<li>metabolite identification<sup id="cite_ref-26" class="reference"><a href="#cite_note-26"><span class="cite-bracket">[</span>26<span class="cite-bracket">]</span></a></sup></li>

<li>pathway databases</li>

<li>2D and 3D protein descriptors<sup id="cite_ref-27" class="reference"><a href="#cite_note-27"><span class="cite-bracket">[</span>27<span class="cite-bracket">]</span></a></sup></li></ul>

<div class="mw-heading mw-heading3"><h3 id="General">General</h3></div>

<ul><li><a href="Python_(programming_language)" title="Python (programming language)">Python</a> wrapper; see Cinfony</li>

<li><a href="Ruby_(programming_language)" title="Ruby (programming language)">Ruby</a> wrapper</li>

<li>active <a href="User_community" class="mw-redirect" title="User community">user community</a></li></ul>

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<ul><li><a href="Bioclipse" title="Bioclipse">Bioclipse</a> – an Eclipse–RCP based chemo-bioinformatics workbench</li>

<li><a href="Blue_Obelisk" title="Blue Obelisk">Blue Obelisk</a></li>

<li><a href="JChemPaint" title="JChemPaint">JChemPaint</a> – Java 2D <a href="Molecule_editor" title="Molecule editor">molecule editor</a>, applet and application</li>

<li><a href="Jmol" title="Jmol">Jmol</a> – Java 3D renderer, applet and application</li>

<li><a href="JOELib" title="JOELib">JOELib</a> – Java version of <a href="Open_Babel" title="Open Babel">Open Babel</a>, <a href="OELib" title="OELib">OELib</a></li>

<li><a href="List_of_free_and_open-source_software_packages" title="List of free and open-source software packages">List of free and open-source software packages</a></li>

<li><a href="List_of_software_for_molecular_mechanics_modeling" class="mw-redirect" title="List of software for molecular mechanics modeling">List of software for molecular mechanics modeling</a></li></ul>

<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

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<li id="cite_note-24"><span class="mw-cite-backlink"><b><a href="#cite_ref-24">^</a></b></span> <span class="reference-text"><cite id="CITEREFPeironcelyRojas-ChertóFicheraReijmers2012" class="citation journal cs1">Peironcely, J. E.; Rojas-Chertó, M.; Fichera, D.; Reijmers, T.; Coulier, L.; Faulon, J. L.; Hankemeier, T. (2012). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558358">"OMG: Open molecule generator"</a>. <i>Journal of Cheminformatics</i>. <b>4</b> (1): 21. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1186%2F1758-2946-4-21">10.1186/1758-2946-4-21</a></span>. <a href="PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558358">3558358</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/22985496">22985496</a>.</cite></span>

</li>

<li id="cite_note-25"><span class="mw-cite-backlink"><b><a href="#cite_ref-25">^</a></b></span> <span class="reference-text"><cite id="CITEREFBashtonNobeliThornton2006" class="citation journal cs1">Bashton, M.; Nobeli, I.; Thornton, J. M. (2006). <a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.jmb.2006.09.041">"Cognate Ligand Domain Mapping for Enzymes"</a>. <i>Journal of Molecular Biology</i>. <b>364</b> (4): <span class="nowrap">836–</span>52. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fj.jmb.2006.09.041">10.1016/j.jmb.2006.09.041</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/17034815">17034815</a>.</cite></span>

</li>

<li id="cite_note-26"><span class="mw-cite-backlink"><b><a href="#cite_ref-26">^</a></b></span> <span class="reference-text"><cite id="CITEREFRojas-ChertoKasperWillighagenVreeken2011" class="citation journal cs1">Rojas-Cherto, M.; Kasper, P. T.; Willighagen, E. L.; Vreeken, R. J.; Hankemeier, T.; Reijmers, T. H. (2011). <a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fbioinformatics%2Fbtr409">"Elemental composition determination based on MSn"</a>. <i>Bioinformatics</i>. <b>27</b> (17): <span class="nowrap">2376–</span>2383. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fbioinformatics%2Fbtr409">10.1093/bioinformatics/btr409</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/21757467">21757467</a>.</cite></span>

</li>

<li id="cite_note-27"><span class="mw-cite-backlink"><b><a href="#cite_ref-27">^</a></b></span> <span class="reference-text"><cite id="CITEREFRuiz-BlancoPazGreenMarrero-Ponce2015" class="citation journal cs1">Ruiz-Blanco, Yasser B; Paz, Waldo; Green, James; Marrero-Ponce, Yovani (2015). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4432771">"ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins"</a>. <i>BMC Bioinformatics</i>. <b>16</b>: 162. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1186%2Fs12859-015-0586-0">10.1186/s12859-015-0586-0</a></span>. <a href="PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4432771">4432771</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/25982853">25982853</a>.</cite></span>

</li>

</ol></div>

<div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2></div>

<ul><li><span class="official-website"><span class="url"><a rel="nofollow" class="external text" href="https://github.com/cdk">Official website</a></span></span></li>

<li><a rel="nofollow" class="external text" href="https://archive.today/20121225081348/http://apps.sourceforge.net/mediawiki/cdk">CDK Wiki</a> – the community wiki</li>

<li><a rel="nofollow" class="external text" href="https://web.archive.org/web/20101107071751/http://pele.farmbio.uu.se/planetcdk/">Planet CDK</a> - a blog planet</li>

<li><a rel="nofollow" class="external text" href="https://www.simolecule.com/cdkdepict/depict.html">CDK Depict</a></li>

<li><a rel="nofollow" class="external text" href="http://www.openscience.org/">OpenScience.org</a></li></ul>

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</style><div id="Computational_chemistry_software280" style="font-size:114%;margin:0 4em"><a href="Computational_chemistry" title="Computational chemistry">Computational chemistry</a> software</div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Cheminformatics" title="Cheminformatics">Cheminformatics</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Free_software" title="Free software">Free software</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="Bioclipse" title="Bioclipse">Bioclipse</a></li>

<li><a href="Blue_Obelisk" title="Blue Obelisk">Blue Obelisk</a></li>

<li><a href="JOELib" title="JOELib">JOELib</a></li>

<li><a href="OELib" title="OELib">OELib</a></li>

<li><a href="Open_Babel" title="Open Babel">Open Babel</a></li>

<li><a href="RDKit" title="RDKit">RDKit</a></li></ul>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Proprietary_software" title="Proprietary software">Proprietary</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="AlvaDesc" title="AlvaDesc">AlvaDesc</a></li>

<li><a href="Schr%C3%B6dinger_(company)" class="mw-redirect" title="Schrödinger (company)">Canvas</a></li>

<li><a href="Chemicalize" title="Chemicalize">Chemicalize</a></li>

<li><a href="Discovery_Studio" title="Discovery Studio">Discovery Studio</a></li>

<li><a href="OpenEye_Scientific_Software" title="OpenEye Scientific Software"> OEChem TK</a></li></ul>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Chemical_kinetics" title="Chemical kinetics">Chemical kinetics</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Free software</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">

<li><a href="Cantera_(software)" title="Cantera (software)">Cantera</a></li>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Proprietary</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="Autochem" title="Autochem">Autochem</a></li>

<li><a href="Chemical_WorkBench" title="Chemical WorkBench">Chemical WorkBench</a></li>

<li><a href="CHEMKIN" title="CHEMKIN">CHEMKIN</a></li>

<li><a href="COSILAB" title="COSILAB">COSILAB</a></li>

<li><a href="DelPhi_(software)" class="mw-redirect" title="DelPhi (software)">DelPhi</a></li>

<li><a href="Khimera" title="Khimera">Khimera</a></li></ul>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Molecular_modelling" title="Molecular modelling">Molecular modelling</a> <br> and <br> <a href="Visualization_(graphics)" title="Visualization (graphics)">visualization</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="List_of_molecular_graphics_systems" title="List of molecular graphics systems">List of molecular graphics systems</a>

</div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Free software</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="Ascalaph_Designer" title="Ascalaph Designer">Ascalaph Designer</a></li>

<li><a href="Avogadro_(software)" title="Avogadro (software)">Avogadro</a></li>

<li><a href="Biskit" title="Biskit">Biskit</a></li>

<li><a href="Gabedit" title="Gabedit">Gabedit</a></li>

<li><a href="Ghemical" title="Ghemical">Ghemical</a></li>

<li><a href="Molekel" title="Molekel">Molekel</a></li>

<li><a href="PyMOL" title="PyMOL">PyMOL</a></li>

<li><a href="QuteMol" title="QuteMol">QuteMol</a></li>

<li><a href="RasMol" title="RasMol">RasMol</a></li></ul>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Proprietary</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="Abalone_(molecular_mechanics)" title="Abalone (molecular mechanics)">Abalone</a></li>

<li><a href="ACD/ChemSketch" title="ACD/ChemSketch">ACD/ChemSketch</a></li>

<li><a href="Atomistix_ToolKit" title="Atomistix ToolKit">Atomistix ToolKit</a></li>

<li><a href="ChemDraw" title="ChemDraw">ChemDraw</a></li>

<li><a href="ChemWindow" title="ChemWindow">ChemWindow</a></li>

<li><a href="EzMol" title="EzMol">EzMol</a></li>

<li><a href="Gaussian_(software)" title="Gaussian (software)">Gaussian</a></li>

<li><a href="Schr%C3%B6dinger_(company)" class="mw-redirect" title="Schrödinger (company)">Maestro</a></li>

<li><a href="MarvinSketch" class="mw-redirect" title="MarvinSketch">MarvinSketch</a></li>

<li><a href="MarvinView" class="mw-redirect" title="MarvinView">MarvinView</a></li>

<li><a href="MODELLER" title="MODELLER">MODELLER</a></li>

<li><a href="Molecular_Operating_Environment" title="Molecular Operating Environment">Molecular Operating Environment</a></li>

<li><a href="SAMSON" title="SAMSON">SAMSON</a></li>

<li><a href="Spartan_(chemistry_software)" title="Spartan (chemistry software)">Spartan</a></li>

<li><a href="UCSF_Chimera" title="UCSF Chimera">UCSF Chimera</a></li>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Docking_(molecular)" title="Docking (molecular)">Molecular docking</a></th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="List_of_protein-ligand_docking_software" title="List of protein-ligand docking software">List of protein-ligand docking software</a>

</div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Free_software" title="Free software">Free software</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="AutoDock" title="AutoDock">AutoDock</a></li>

<li><a href="AutoDock_Vina" class="mw-redirect" title="AutoDock Vina">AutoDock Vina</a></li>

<li><a href="FlexAID" title="FlexAID">FlexAID</a></li>

<li><a href="RDock" title="RDock">rDock</a></li></ul>

<ul><li><a href="Glide_(docking)" title="Glide (docking)">Glide</a></li>

<li><a href="LeDock" title="LeDock">LeDock</a></li>

<li><a href="Molecular_Operating_Environment" title="Molecular Operating Environment">Molecular Operating Environment</a></li>

<li><a href="OpenEye_Scientific_Software" title="OpenEye Scientific Software"> OEDocking</a></li></ul>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Molecular_dynamics" title="Molecular dynamics">Molecular dynamics</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Free_software" title="Free software">Free software</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">

<li><a href="GROMACS" title="GROMACS">GROMACS</a></li>

<li><a href="LAMMPS" title="LAMMPS">LAMMPS</a></li>

<li><a href="OpenMM" title="OpenMM">OpenMM</a></li>

<li><a href="PLUMED" title="PLUMED">PLUMED</a></li></ul>

<ul><li><a href="Abalone_(molecular_mechanics)" title="Abalone (molecular mechanics)">Abalone</a></li>

<li><a href="AMBER" title="AMBER">AMBER</a></li>

<li><a href="CHARMM" title="CHARMM">CHARMM</a></li>

<li><a href="Desmond_(software)" title="Desmond (software)">Desmond</a></li>

<li><a href="GROMOS" title="GROMOS">GROMOS</a></li>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Quantum_chemistry" title="Quantum chemistry">Quantum chemistry</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"><a href="List_of_quantum_chemistry_and_solid-state_physics_software" title="List of quantum chemistry and solid-state physics software">List of quantum chemistry and solid-state physics software</a>

<ul><li><a href="ABINIT" title="ABINIT">ABINIT</a></li>

<li><a href="ACES_(computational_chemistry)" title="ACES (computational chemistry)">ACES</a> (CFOUR)</li>

<li><a href="AIMAll" title="AIMAll">AIMAll</a></li>

<li><a href="BigDFT" title="BigDFT">BigDFT</a></li>

<li><a href="COLUMBUS" title="COLUMBUS">COLUMBUS</a></li>

<li><a href="CONQUEST" title="CONQUEST">CONQUEST</a></li>

<li><a href="Dalton_(program)" title="Dalton (program)">Dalton</a></li>

<li><a href="Dirac_(software)" title="Dirac (software)">DIRAC</a></li>

<li><a href="FLEUR" title="FLEUR">FLEUR</a></li>

<li><a href="FreeON" title="FreeON">FreeON</a></li>

<li><a href="MADNESS" title="MADNESS">MADNESS</a></li>

<li><a href="MOPAC" title="MOPAC">MOPAC</a></li>

<li><a href="NWChem" title="NWChem">NWChem</a></li>

<li><a href="Octopus_(software)" title="Octopus (software)">Octopus</a></li>

<li><a href="MOLCAS" title="MOLCAS">OpenMolcas</a></li>

<li><a href="PARSEC" title="PARSEC">PARSEC</a></li>

<li>PyQuante</li>

<li><a href="PySCF" title="PySCF">PySCF</a></li>

<li><a href="Quantum_ESPRESSO" title="Quantum ESPRESSO">Quantum ESPRESSO</a> (PWscf)</li>

<li><a href="SIESTA_(computer_program)" title="SIESTA (computer program)">SIESTA</a></li>

<li><a href="YAMBO_code" title="YAMBO code">YAMBO code</a></li></ul>

<li><a href="AMPAC" title="AMPAC">AMPAC</a></li>

<li><a href="CADPAC" title="CADPAC">CADPAC</a></li>

<li><a href="CASINO" title="CASINO">CASINO</a></li>

<li><a href="CASTEP" title="CASTEP">CASTEP</a></li>

<li><a href="Valence_bond_programs" title="Valence bond programs">CRUNCH</a></li>

<li><a href="CRYSTAL_(software)" title="CRYSTAL (software)">CRYSTAL</a></li>

<li><a href="Firefly_(computer_program)" title="Firefly (computer program)">Firefly</a></li>

<li><a href="GAMESS_(UK)" title="GAMESS (UK)">GAMESS (UK)</a></li>

<li><a href="GAMESS_(US)" title="GAMESS (US)">GAMESS (US)</a></li>

<li><a href="Gaussian_(software)" title="Gaussian (software)">Gaussian</a></li>

<li><a href="Jaguar_(software)" title="Jaguar (software)">Jaguar</a></li>

<li><a href="MOLCAS" title="MOLCAS">MOLCAS</a></li>

<li><a href="MOLPRO" title="MOLPRO">MOLPRO</a></li>

<li><a href="ONETEP" title="ONETEP">ONETEP</a></li>

<li><a href="OpenAtom" title="OpenAtom">OpenAtom</a></li>

<li><a href="PLATO_(computational_chemistry)" title="PLATO (computational chemistry)">PLATO</a></li>

<li><a href="Quantemol" title="Quantemol">Quantemol</a></li>

<li><a href="Scigress" title="Scigress">Scigress</a></li>

<li><a href="Spartan_(chemistry_software)" title="Spartan (chemistry software)">Spartan</a></li>

<li><a href="TeraChem" title="TeraChem">TeraChem</a></li>

<li><a href="TURBOMOLE" title="TURBOMOLE">TURBOMOLE</a></li>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Skeletal_structure" class="mw-redirect" title="Skeletal structure">Skeletal structure</a> drawing</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Free software</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="JChemPaint" title="JChemPaint">JChemPaint</a></li>

<li><a href="Molsketch" class="mw-redirect" title="Molsketch">Molsketch</a></li>

<li><a href="XDrawChem" title="XDrawChem">XDrawChem</a></li></ul>

<ul><li><a href="ACD/ChemSketch" title="ACD/ChemSketch">ACD/ChemSketch</a></li>

<li><a href="ISIS/Draw" title="ISIS/Draw">BIOVIA Draw</a></li>

<li>ChemDoodle</li>

<li><a href="ChemDraw" title="ChemDraw">ChemDraw</a></li>

<li><a href="ChemWindow" title="ChemWindow">ChemWindow</a></li>

<li><a href="JME_Molecule_Editor" title="JME Molecule Editor">JME Molecule Editor</a></li>

<li><a href="MarvinSketch" class="mw-redirect" title="MarvinSketch">MarvinSketch</a></li>

<li><a href="OpenEye_Scientific_Software" title="OpenEye Scientific Software"> PICTO</a></li></ul>

</div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Others</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="Aqion" title="Aqion">Aqion</a></li>

<li><a href="Mercury_(crystallography)" title="Mercury (crystallography)">Mercury</a></li>

<li><a href="CrystalExplorer" title="CrystalExplorer">CrystalExplorer</a></li>

<li><a href="Internal_Coordinate_Mechanics" title="Internal Coordinate Mechanics">ICM</a> (ICM-Browser)</li>

<li><a href="Materials_Studio" title="Materials Studio">Materials Studio</a></li>

<li><a href="Molden" title="Molden">Molden</a></li>

<li><a href="OpenChrom" title="OpenChrom">OpenChrom</a></li>

<li>SASHIMI</li></ul>

</div></td></tr></tbody></table></div></div><div><div class="zim-footer">

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