OpenEye Scientific Software is an American software company founded by
Anthony Nicholls in 1997. It develops large-scale
molecular modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials scien ...
applications and
toolkits. Following OpenEye's acquisition by
Cadence Design Systems
Cadence Design Systems, Inc. (stylized as cādence)Investor's Business DailCEO Lip-Bu Tan Molds Troubled Cadence Into Long-Term LeaderRetrieved November 12, 2020 is an American multinational corporation, multinational technology and computational ...
for $500million in September 2022, the company was rebranded to OpenEye Cadence Molecular Sciences and operates as a business unit under Cadence.
Scope
Primarily geared towards
drug discovery
In the fields of medicine, biotechnology, and pharmacology, drug discovery is the process by which new candidate medications are discovered.
Historically, drugs were discovered by identifying the active ingredient from traditional remedies or ...
and
design
A design is the concept or proposal for an object, process, or system. The word ''design'' refers to something that is or has been intentionally created by a thinking agent, and is sometimes used to refer to the inherent nature of something ...
, areas of application include conformation generation,
docking, shape comparison,
charge
Charge or charged may refer to:
Arts, entertainment, and media Films
* ''Charge, Zero Emissions/Maximum Speed'', a 2011 documentary
Music
* ''Charge'' (David Ford album)
* ''Charge'' (Machel Montano album)
* '' Charge!!'', an album by The Aqu ...
/
electrostatics
Electrostatics is a branch of physics that studies slow-moving or stationary electric charges.
Since classical antiquity, classical times, it has been known that some materials, such as amber, attract lightweight particles after triboelectric e ...
,
cheminformatics
Cheminformatics (also known as chemoinformatics) refers to the use of physical chemistry theory with computer and information science techniques—so called "'' in silico''" techniques—in application to a range of descriptive and prescriptive ...
and visualization. The software is designed for scientific rigor, as well as speed, scalability and
platform independence.
OpenEye makes much of its technology available as
toolkits suitable for custom development. The toolkits are available in multiple languages:
C++,
Python,
Java
Java is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea (a part of Pacific Ocean) to the north. With a population of 156.9 million people (including Madura) in mid 2024, proje ...
and
C#.
Application software
* AFITT -
Crystallographic
Crystallography is the branch of science devoted to the study of molecular and crystalline structure and properties. The word ''crystallography'' is derived from the Ancient Greek word (; "clear ice, rock-crystal"), and (; "to write"). In J ...
refinement and analysis.
* BROOD -
Bioisostere
In medicinal chemistry, bioisosteres are chemical substituents or groups with similar physical or chemical properties which produce broadly similar biological properties in the same chemical compound. In drug design, the purpose of exchanging one b ...
identification using shape, chemistry and
electrostatic similarity.
* EON -
Chemical
A chemical substance is a unique form of matter with constant chemical composition and characteristic properties. Chemical substances may take the form of a single element or chemical compounds. If two or more chemical substances can be combin ...
similarity analysis via comparison of
electrostatics overlay.
* FastROCS - Real-time 3D molecular shape searches, using GPU technology.
* FILTER -
Molecular
A molecule is a group of two or more atoms that are held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemistry, ...
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
A molecule is a group of two or more atoms that are held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemistry ...
and
proteins
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, re ...
.
* ROCS -
Chemical similarity
Chemical similarity (or molecular similarity) refers to the similarity of chemical elements, molecules or chemical compounds with respect to either structural or functional qualities, i.e. the effect that the chemical compound has on reaction partn ...
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 coordination chemistry, a ligand is an ion or molecule with a functional group that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's ...
in
gas-phase
Gas is a state of matter that has neither a fixed volume nor a fixed shape and is a compressibility, compressible fluid. A ''pure gas'' is made up of individual atoms (e.g. a noble gas like neon) or molecules of either a single type of atom (ch ...
,
solution
Solution may refer to:
* Solution (chemistry), a mixture where one substance is dissolved in another
* Solution (equation), in mathematics
** Numerical solution, in numerical analysis, approximate solutions within specified error bounds
* Solu ...
, 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
Electrostatics is a branch of physics that studies slow-moving or stationary electric charges.
Since classical antiquity, classical times, it has been known that some materials, such as amber, attract lightweight particles after triboelectric e ...
solver.
See also
*
Computational chemistry
Computational chemistry is a branch of chemistry that uses computer simulations to assist in solving chemical problems. It uses methods of theoretical chemistry incorporated into computer programs to calculate the structures and properties of mol ...
References
*
*
*
* https://docs.eyesopen.com/toolkits/python/intro.html
External links
* {{official website, http://www.eyesopen.com/
Biotechnology companies of the United States
Companies based in Santa Fe, New Mexico
American corporate subsidiaries
Software companies based in New Mexico
Software companies established in 1997
Software companies of the United States
2022 mergers and acquisitions