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<title>OpenEye Scientific Software</title>

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<span id="openzim-page-title" class="mw-page-title-main"><span class="mw-page-title-main">OpenEye Scientific Software</span></span>

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</style><table class="infobox ib-company vcard"><caption class="infobox-title fn org" style="font-size: 125%;">OpenEye Scientific Software</caption><tbody><tr><td colspan="2" class="infobox-image ib-company-logo logo"></td></tr><tr><th scope="row" class="infobox-label">Company type</th><td class="infobox-data category"><a href="Subsidiary" title="Subsidiary">Subsidiary</a></td></tr><tr><th scope="row" class="infobox-label">Industry</th><td class="infobox-data category"><style data-mw-deduplicate="TemplateStyles:r1126788409">

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</style><div class="plainlist"><ul><li><a href="Computer_software" class="mw-redirect" title="Computer software">Computer software</a></li><li><a href="Research_and_development" title="Research and development">Research and development</a></li><li><a href="Biotechnology" title="Biotechnology">Biotechnology</a></li><li><a href="Cheminformatics" title="Cheminformatics">Cheminformatics</a></li></ul></div></td></tr><tr><th scope="row" class="infobox-label">Founded</th><td class="infobox-data">1997<span style="display:none"> (<span class="bday dtstart published updated">1997</span>)</span></td></tr><tr><th scope="row" class="infobox-label">Founder</th><td class="infobox-data agent"><a href="Anthony_Nicholls_(physicist)" title="Anthony Nicholls (physicist)">Anthony Nicholls</a><sup id="cite_ref-sfnm_1-0" class="reference"><a href="#cite_note-sfnm-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup></td></tr><tr><th scope="row" class="infobox-label">Headquarters</th><td class="infobox-data adr"><div class="ib-company-locality locality"><a href="Santa_Fe%2C_New_Mexico" title="Santa Fe, New Mexico">Santa Fe, New Mexico</a></div>, <div class="ib-company-country country-name">United States</div></td></tr><tr><th scope="row" class="infobox-label"><div style="display: inline-block; line-height: 1.2em; padding: .1em 0;">Key people</div></th><td class="infobox-data agent">Anthony Nicholls (CEO)<sup id="cite_ref-sfnm_1-1" class="reference"><a href="#cite_note-sfnm-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup></td></tr><tr><th scope="row" class="infobox-label"><div style="display: inline-block; line-height: 1.2em; padding: .1em 0;">Number of employees</div></th><td class="infobox-data">130 (2022)<sup id="cite_ref-sfnm_1-2" class="reference"><a href="#cite_note-sfnm-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup></td></tr><tr><th scope="row" class="infobox-label"><a href="Parent_company" class="mw-redirect" title="Parent company">Parent</a></th><td class="infobox-data"><a href="Cadence_Design_Systems" title="Cadence Design Systems">Cadence Design Systems</a></td></tr><tr><th scope="row" class="infobox-label">Website</th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="http://www.eyesopen.com/">www<wbr>.eyesopen<wbr>.com</a></span></td></tr></tbody></table>

<p><b>OpenEye Scientific Software</b> is an American software company founded by <a href="Anthony_Nicholls_(physicist)" title="Anthony Nicholls (physicist)">Anthony Nicholls</a> in 1997.<sup id="cite_ref-sfnm_1-3" class="reference"><a href="#cite_note-sfnm-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> It develops large-scale <a href="Molecular_modelling" title="Molecular modelling">molecular modelling</a> <a href="Computer_application" class="mw-redirect" title="Computer application">applications</a> and <a href="Programming_library" class="mw-redirect" title="Programming library">toolkits</a>. Following OpenEye's acquisition by <a href="Cadence_Design_Systems" title="Cadence Design Systems">Cadence Design Systems</a> for $500<span class="nowrap"> </span>million in September 2022, the company was rebranded to OpenEye Cadence Molecular Sciences and operates as a business unit under Cadence.<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><sup id="cite_ref-sfnm_1-4" class="reference"><a href="#cite_note-sfnm-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup>

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

<p>Primarily geared towards <a href="Drug_discovery" title="Drug discovery">drug discovery</a> and <a href="Drug_design" title="Drug design">design</a>, areas of application include conformation generation, <a href="Docking_(molecular)" title="Docking (molecular)">docking</a>, shape comparison, <a href="Charge_(physics)" title="Charge (physics)">charge</a>/<a href="Electrostatics" title="Electrostatics">electrostatics</a>, <a href="Cheminformatics" title="Cheminformatics">cheminformatics</a> and visualization. The software is designed for scientific rigor, as well as speed, scalability and <a href="Platform_(computing)" class="mw-redirect" title="Platform (computing)">platform independence</a>.

</p><p>OpenEye makes much of its technology available as <a href="Programming_library" class="mw-redirect" title="Programming library">toolkits</a> suitable for custom development. The toolkits are available in multiple languages: <a href="C%2B%2B" title="C++">C++</a>, <a href="Python_(programming_language)" title="Python (programming language)">Python</a>, <a href="Java_(programming_language)" title="Java (programming language)">Java</a> and <a href="C_Sharp_(programming_language)" title="C Sharp (programming language)">C#</a>.

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<div class="mw-heading mw-heading2"><h2 id="Application_software">Application software</h2></div>

<ul><li>AFITT - <a href="Crystallographic" class="mw-redirect" title="Crystallographic">Crystallographic</a> refinement and analysis.</li>

<li>BROOD - <a href="Bioisostere" title="Bioisostere">Bioisostere</a> identification using shape, chemistry and <a href="Electrostatics" title="Electrostatics">electrostatic similarity</a>.</li>

<li>EON - <a href="Chemical_substance" title="Chemical substance">Chemical</a> similarity analysis via comparison of <a href="Electrostatics" title="Electrostatics">electrostatics overlay</a>.</li>

<li>FastROCS - Real-time 3D molecular shape searches, using GPU technology.</li>

<li>FILTER - <a href="Molecule" title="Molecule">Molecular</a> screening and selection based on physical property or functional group.</li>

<li>OEDocking - Molecular docking tools including FRED (fast docking), HYBRID (ligand guided docking) and POSIT (ligand guided pose prediction).</li>

<li>OMEGA - Fast, accurate <a href="Conformer_generation" class="mw-redirect" title="Conformer generation">conformer generation</a>, for linear and macrocyclic molecules.</li>

<li>pKa Prospector - A database of high quality pKa measurements.</li>

<li>QUACPAC - Tautomers, protonation states and charges for small <a href="Molecules" class="mw-redirect" title="Molecules">molecules</a> and <a href="Proteins" class="mw-redirect" title="Proteins">proteins</a>.</li>

<li>ROCS - <a href="Chemical_substance" title="Chemical substance">Chemical similarity</a> analysis via rapid 3D molecular shape searches.</li>

<li>SZMAP - Identify water sites in a protein binding site for improving ligand potency.</li>

<li>SZYBKI - Fast forcefield optimization of <a href="Ligands" class="mw-redirect" title="Ligands">ligands</a> in <a href="Gas-phase" class="mw-redirect" title="Gas-phase">gas-phase</a>, <a href="Solution_(chemistry)" title="Solution (chemistry)">solution</a>, or within a <a href="Protein_active_site" class="mw-redirect" title="Protein active site">protein active site</a>.</li>

<li>VIDA - Graphical user interface that visualizes, analyzes and manages corporate collections of <a href="Molecular_structures" class="mw-redirect" title="Molecular structures">molecular structures</a> and information.</li></ul>

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

<p>Programming libraries providing wider applications with object-oriented accessibility to a given set of capabilities.

</p>

<ul><li>OEChem TK - Core molecule handling, cheminformatics and 3D molecular data handling.</li>

<li>Bioisostere TK - 3D fragment replacement.</li>

<li>OEDepict TK - 2D molecule rendering and depiction.</li>

<li>OEDocking TK - Molecular docking and scoring.</li>

<li>OEFF TK - Molecule objective functions, adaptors and optimizers.</li>

<li>Grapheme TK - Render complex 3D information into 2D for simplified analysis.</li>

<li>GraphSim TK - 2D molecular fingerprints and similarity calculations.</li>

<li>EON TK - 3D electrostatics description, optimization and overlap comparisons.</li>

<li>FastROCS TK - extremely fast shape comparisons.</li>

<li>Lexichem TK - State-of-the-art compound name and structure interconversion with support for multiple foreign languages.</li>

<li>MolProp TK - Molecular property calculation and filtering.</li>

<li>MedChem TK - Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics.</li>

<li>Quacpac TK - Tautomer enumeration and charge assignment.</li>

<li>Omega TK - Rapid, accurate conformer generation.</li>

<li>Shape TK - 3D molecular shape description, optimization and overlap comparisons.</li>

<li>Sitehopper TK - Rapid binding site comparison, GPU enabled.</li>

<li>Spicoli TK - Rapid molecular surface generation, manipulation and interrogation.</li>

<li>Spruce TK - Protein preparation and modeling.</li>

<li>Szmap TK - Understanding water interactions in a protein binding site.</li>

<li>Szykbi TK - Molecular energetics with forcefields. Generalized function optimization, e.g. molecular structure optimization.</li>

<li>Zap TK - An efficient <a href="Poisson-Boltzmann" class="mw-redirect" title="Poisson-Boltzmann">Poisson-Boltzmann</a> <a href="Electrostatics" title="Electrostatics">electrostatics</a> solver.</li></ul>

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<ul><li><a href="Computational_chemistry" title="Computational chemistry">Computational chemistry</a></li></ul>

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

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</style><cite id="CITEREFVitu2022" class="citation news cs1">Vitu, Teya (August 23, 2022). <a rel="nofollow" class="external text" href="https://www.santafenewmexican.com/news/business/silicon-valley-firm-seeks-to-acquire-santa-fes-openeye-scientific/article_a8c599e8-1f0b-11ed-bc14-f748409bb197.html">"Silicon Valley firm seeks to acquire Santa Fe's OpenEye Scientific"</a>. <i><a href="The_Santa_Fe_New_Mexican" title="The Santa Fe New Mexican">The Santa Fe New Mexican</a></i>.</cite></span>

</li>

<li id="cite_note-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-2">^</a></b></span> <span class="reference-text"><cite id="CITEREFKeller2022" class="citation news cs1">Keller, Chris (September 1, 2022). <a rel="nofollow" class="external text" href="https://www.bizjournals.com/albuquerque/inno/stories/news/2022/09/01/openeye-scientific-acquired-500-million-deal.html">"Santa Fe-based company acquired in deal valued at about $500M"</a>. <a href="American_City_Business_Journals" title="American City Business Journals">American City Business Journals</a>.</cite></span>

</li>

</ol></div></div>

<ul><li><cite class="citation web cs1"><a rel="nofollow" class="external text" href="http://www.genomeweb.com/informatics/downloads-and-upgrades-afitt-23-genbank-1970-and-protein-databank">"Downloads and Upgrades: AFITT 2.3, GenBank 197.0, and the Protein Databank"</a>. <i>BioInform</i>. Genomeweb LLC. August 16, 2013<span class="reference-accessdate">. Retrieved <span class="nowrap">August 28,</span> 2013</span>.</cite></li>

<li><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://web.archive.org/web/20090305233831/http://investing.businessweek.com/research/stocks/private/snapshot.asp?privcapId=27568910">"Company Overview of OpenEye Scientific Software, Inc"</a>. <i>Bloomberg Businessweek</i>. Bloomberg L.P. Archived from <a rel="nofollow" class="external text" href="http://investing.businessweek.com/research/stocks/private/snapshot.asp?privcapId=27568910">the original</a> on March 5, 2009<span class="reference-accessdate">. Retrieved <span class="nowrap">August 28,</span> 2013</span>.</cite></li>

<li><cite id="CITEREFYang2011" class="citation web cs1">Yang, Jeremy J. (Fall 2011). <a rel="nofollow" class="external text" href="http://homes.soic.indiana.edu/jejyang/misc/cheminfo_software_devel.pdf">"Cheminformatics Software Development: Case Studies"</a> <span class="cs1-format">(PDF)</span>. Indiana University School of Informatics and Computing<span class="reference-accessdate">. Retrieved <span class="nowrap">August 28,</span> 2013</span>.</cite></li>

<li><a rel="nofollow" class="external free" href="https://docs.eyesopen.com/toolkits/python/intro.html">https://docs.eyesopen.com/toolkits/python/intro.html</a></li></ul>

<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="http://www.eyesopen.com/">Official website</a></span></span></li></ul></div><div><div class="zim-footer">

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