OpenEye Scientific Software

Type| Subsidiary
Industry|

* Computer software
* Research and development
* Biotechnology
* Cheminformatics

Founded| 1997; 29 years ago (1997)
Founder| Anthony Nicholls[1]
Headquarters|

Santa Fe, New Mexico

United States

Key people

| Anthony Nicholls (CEO)[1]

Number of employees

| 130 (2022)[1]
Parent| Cadence Design Systems
Website| www.eyesopen.com

OpenEye Scientific Software is an American software company founded by Anthony Nicholls in 1997.[1] It develops large-scale molecular modelling applications and toolkits. Following OpenEye's acquisition by Cadence Design Systems for $500 million in September 2022, the company was rebranded to OpenEye Cadence Molecular Sciences and operates as a business unit under Cadence.[2][1]

## Contents

* 1 Scope
* 2 Application software
* 3 Toolkits
* 4 See also
* 5 References
* 6 External links

## Scope

Primarily geared towards drug discovery and design, areas of application include conformation generation, docking, shape comparison, charge/electrostatics, cheminformatics and visualization. The software is designed for scientific rigor, as well as speed, scalability and platform independence.

## Application software

* AFITT - Crystallographic refinement and analysis.
* BROOD - Bioisostere identification using shape, chemistry and electrostatic similarity.
* EON - Chemical similarity analysis via comparison of electrostatics overlay.
* FastROCS - Real-time 3D molecular shape searches, using GPU technology.
* FILTER - Molecular screening and selection based on physical property or functional group.
* OEDocking - Molecular docking tools including FRED (fast docking), HYBRID (ligand guided docking) and POSIT (ligand guided pose prediction).
* OMEGA - Fast, accurate conformer generation, for linear and macrocyclic molecules.
* pKa Prospector - A database of high quality pKa measurements.
* QUACPAC - Tautomers, protonation states and charges for small molecules and proteins.
* ROCS - Chemical similarity analysis via rapid 3D molecular shape searches.
* SZMAP - Identify water sites in a protein binding site for improving ligand potency.
* SZYBKI - Fast forcefield optimization of ligands in gas-phase, solution, or within a protein active site.
* VIDA - Graphical user interface that visualizes, analyzes and manages corporate collections of molecular structures and information.

## Toolkits

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

* OEChem TK - Core molecule handling, cheminformatics and 3D molecular data handling.
* Bioisostere TK - 3D fragment replacement.
* OEDepict TK - 2D molecule rendering and depiction.
* OEDocking TK - Molecular docking and scoring.
* OEFF TK - Molecule objective functions, adaptors and optimizers.
* Grapheme TK - Render complex 3D information into 2D for simplified analysis.
* GraphSim TK - 2D molecular fingerprints and similarity calculations.
* EON TK - 3D electrostatics description, optimization and overlap comparisons.
* FastROCS TK - extremely fast shape comparisons.
* Lexichem TK - State-of-the-art compound name and structure interconversion with support for multiple foreign languages.
* MolProp TK - Molecular property calculation and filtering.
* MedChem TK - Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics.
* Quacpac TK - Tautomer enumeration and charge assignment.
* Omega TK - Rapid, accurate conformer generation.
* Shape TK - 3D molecular shape description, optimization and overlap comparisons.
* Sitehopper TK - Rapid binding site comparison, GPU enabled.
* Spicoli TK - Rapid molecular surface generation, manipulation and interrogation.
* Spruce TK - Protein preparation and modeling.
* Szmap TK - Understanding water interactions in a protein binding site.
* Szykbi TK - Molecular energetics with forcefields. Generalized function optimization, e.g. molecular structure optimization.
* Zap TK - An efficient Poisson-Boltzmann electrostatics solver.

## See also

* Computational chemistry

## References

1. ↑ 1.0 1.1 1.2 1.3 1.4 Vitu, Teya (August 23, 2022). "Silicon Valley firm seeks to acquire Santa Fe's OpenEye Scientific". The Santa Fe New Mexican. https://www.santafenewmexican.com/news/business/silicon-valley-firm-seeks-to-acquire-santa-fes-openeye-scientific/article_a8c599e8-1f0b-11ed-bc14-f748409bb197.html.
2. ↑ Keller, Chris (September 1, 2022). "Santa Fe-based company acquired in deal valued at about $500M". American City Business Journals. https://www.bizjournals.com/albuquerque/inno/stories/news/2022/09/01/openeye-scientific-acquired-500-million-deal.html.

* "Downloads and Upgrades: AFITT 2.3, GenBank 197.0, and the Protein Databank". BioInform. Genomeweb LLC. August 16, 2013. http://www.genomeweb.com/informatics/downloads-and-upgrades-afitt-23-genbank-1970-and-protein-databank. Retrieved August 28, 2013.
* "Company Overview of OpenEye Scientific Software, Inc.". Bloomberg Businessweek. Bloomberg L.P.. http://investing.businessweek.com/research/stocks/private/snapshot.asp?privcapId=27568910. Retrieved August 28, 2013.
* Yang, Jeremy J. (Fall 2011). "Cheminformatics Software Development: Case Studies". Indiana University School of Informatics and Computing. http://homes.soic.indiana.edu/jejyang/misc/cheminfo_software_devel.pdf. Retrieved August 28, 2013.
* https://docs.eyesopen.com/toolkits/python/intro.html

## External links

* Official website

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