OpenEye Scientific Software

<h2 id="scope">Scope</h2>
<p>Primarily geared towards <a href="/facts/Drug_discovery/LLdDNvjy">drug discovery</a> and <a href="/facts/Drug_design/XAU0Ke3d">design</a>, areas of application include conformation generation, <a href="/facts/Docking_(molecular)/IKzf94wQ">docking</a>, shape comparison, <a href="/facts/Charge_(physics)/jnQEDBI3">charge</a>/<a href="/facts/Electrostatics/bxkuW6s4">electrostatics</a>, <a href="/facts/Cheminformatics/BwBkT11c">cheminformatics</a> and visualization. The software is designed for scientific rigor, as well as speed, scalability and <a href="/facts/Platform_(computing)/DmKwp5Bk">platform independence</a>.
</p><p>OpenEye makes much of its technology available as <a href="/facts/Programming_library/xRzL3P7q">toolkits</a> suitable for custom development. The toolkits are available in multiple languages: <a href="/facts/C%252B%252B/Et0F2qn9">C++</a>, <a href="/facts/Python_(programming_language)/YbuGqofa">Python</a>, <a href="/facts/Java_(programming_language)/9ScgFyAL">Java</a> and <a href="/facts/C_Sharp_(programming_language)/UC2gxeyb">C#</a>.
</p>
<h2 id="application-software">Application software</h2>
<ul><li>AFITT - <a href="/facts/Crystallographic/9B5toeqG">Crystallographic</a> refinement and analysis.</li>
<li>BROOD - <a href="/facts/Bioisostere/M7R0LGfp">Bioisostere</a> identification using shape, chemistry and <a href="/facts/Electrostatics/bxkuW6s4">electrostatic similarity</a>.</li>
<li>EON - <a href="/facts/Chemical_substance/EWcXU41d">Chemical</a> similarity analysis via comparison of <a href="/facts/Electrostatics/bxkuW6s4">electrostatics overlay</a>.</li>
<li>FastROCS - Real-time 3D molecular shape searches, using GPU technology.</li>
<li>FILTER - <a href="/facts/Molecule/N9ljSfFq">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="/facts/Conformer_generation/JflrT5Ws">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="/facts/Molecules/N9ljSfFq">molecules</a> and <a href="/facts/Proteins/Jxmagu3E">proteins</a>.</li>
<li>ROCS - <a href="/facts/Chemical_substance/EWcXU41d">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="/facts/Ligands/6etB3qeW">ligands</a> in <a href="/facts/Gas-phase/hVVAoodV">gas-phase</a>, <a href="/facts/Solution_(chemistry)/MGchhMQV">solution</a>, or within a <a href="/facts/Protein_active_site/Jxmagu3E">protein active site</a>.</li>
<li>VIDA - Graphical user interface that visualizes, analyzes and manages corporate collections of <a href="/facts/Molecular_structures/7USG5zDn">molecular structures</a> and information.</li></ul>
<h2 id="toolkits">Toolkits</h2>
<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="/facts/Poisson-Boltzmann/Hn0mUng9">Poisson-Boltzmann</a> <a href="/facts/Electrostatics/bxkuW6s4">electrostatics</a> solver.</li></ul>
<h2 id="see-also">See also</h2>
<ul>
<li>Companies portal</li></ul>
<ul><li><a href="/facts/Computational_chemistry/KyuCgRV3">Computational chemistry</a></li></ul>

<ul><li><a 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. Retrieved August 28, 2013.</li>
<li><a 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 href="http://investing.businessweek.com/research/stocks/private/snapshot.asp?privcapId=27568910">the original</a> on March 5, 2009. Retrieved August 28, 2013.</li>
<li>Yang, Jeremy J. (Fall 2011). <a href="http://homes.soic.indiana.edu/jejyang/misc/cheminfo_software_devel.pdf">"Cheminformatics Software Development: Case Studies"</a> (PDF). Indiana University School of Informatics and Computing. Retrieved August 28, 2013.</li>
<li><a href="https://docs.eyesopen.com/toolkits/python/intro.html">https://docs.eyesopen.com/toolkits/python/intro.html</a></li></ul>
<h2 id="external-links">External links</h2>
<ul><li><a href="http://www.eyesopen.com/">Official website</a></li></ul>

<h2 id="references">References</h2>

<ol>
<li id="fn:1"><p>Vitu, Teya (August 23, 2022). "Silicon Valley firm seeks to acquire Santa Fe's OpenEye Scientific". The Santa Fe New Mexican. <a href="https://www.santafenewmexican.com/news/business/silicon-valley-firm-seeks-to-acquire-santa-fes-openeye-scientific/article_a8c599e8-1f0b-11ed-bc14-f748409bb197.html" target="_blank">https://www.santafenewmexican.com/news/business/silicon-valley-firm-seeks-to-acquire-santa-fes-openeye-scientific/article_a8c599e8-1f0b-11ed-bc14-f748409bb197.html</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li>
<li id="fn:2"><p>Keller, Chris (September 1, 2022). "Santa Fe-based company acquired in deal valued at about $500M". American City Business Journals. <a href="https://www.bizjournals.com/albuquerque/inno/stories/news/2022/09/01/openeye-scientific-acquired-500-million-deal.html" target="_blank">https://www.bizjournals.com/albuquerque/inno/stories/news/2022/09/01/openeye-scientific-acquired-500-million-deal.html</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li>
<li id="fn:3"><p>Vitu, Teya (August 23, 2022). "Silicon Valley firm seeks to acquire Santa Fe's OpenEye Scientific". The Santa Fe New Mexican. <a href="https://www.santafenewmexican.com/news/business/silicon-valley-firm-seeks-to-acquire-santa-fes-openeye-scientific/article_a8c599e8-1f0b-11ed-bc14-f748409bb197.html" target="_blank">https://www.santafenewmexican.com/news/business/silicon-valley-firm-seeks-to-acquire-santa-fes-openeye-scientific/article_a8c599e8-1f0b-11ed-bc14-f748409bb197.html</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li>
</ol>

OpenEye Scientific Software open-in-new

OpenEye Scientific Software