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 sci ...
applications and
toolkits. In July 2022,
Cadence Design Systems
Cadence Design Systems, Inc. (stylized as cādence), headquartered in San Jose, California, is an American multinational corporation, multinational computational software company, founded in 1988 by the merger of SDA Systems and ECAD, Inc. The co ...
agreed to acquire OpenEye for $500million in cash.
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 by ...
and
design
A design is a plan or specification for the construction of an object or system or for the implementation of an activity or process or the result of that plan or specification in the form of a prototype, product, or process. The verb ''to design'' ...
, 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 Aqua ...
/
electrostatics
Electrostatics is a branch of physics that studies electric charges at rest (static electricity).
Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amber ...
,
cheminformatics
Cheminformatics (also known as chemoinformatics) refers to 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 problem ...
and visualization. The software is designed for scientific rigor, as well as speed, scalability and
platform independence
In computing, cross-platform software (also called multi-platform software, platform-agnostic software, or platform-independent software) is computer software that is designed to work in several computing platforms. Some cross-platform software r ...
.
OpenEye makes much of its technology available as
toolkits suitable for custom development. The toolkits are available in multiple languages:
C++
C++ (pronounced "C plus plus") is a high-level general-purpose programming language created by Danish computer scientist Bjarne Stroustrup as an extension of the C programming language, or "C with Classes". The language has expanded significan ...
,
Python
Python may refer to:
Snakes
* Pythonidae, a family of nonvenomous snakes found in Africa, Asia, and Australia
** ''Python'' (genus), a genus of Pythonidae found in Africa and Asia
* Python (mythology), a mythical serpent
Computing
* Python (pro ...
,
Java
Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's List ...
and
C#.
Application software
* AFITT -
Crystallographic
Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics (condensed matter physics). The word ...
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 to another chemical compound. In drug design, the purpose of exchanging one bi ...
identification using shape, chemistry and
electrostatic similarity.
* EON -
Chemical
A chemical substance is a form of matter having constant chemical composition and characteristic properties. Some references add that chemical substance cannot be separated into its constituent elements by physical separation methods, i.e., wi ...
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 held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...
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
In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation). While any two arrangements of atoms in a mo ...
, 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 held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...
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, respo ...
.
* 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 (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 electro ...
in
gas-phase
Gas is one of the four fundamental states of matter (the others being solid, liquid, and plasma).
A pure gas may be made up of individual atoms (e.g. a noble gas like neon), elemental molecules made from one type of atom (e.g. oxygen), or com ...
,
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
* Soluti ...
, or within a
protein active site.
* VIDA - Graphical user interface that visualizes, analyzes and manages corporate collections of
molecular structures
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that deter ...
and information.
Toolkits
Programming libraries providing other applications with object-oriented accessibility to a given set of capabilities.
* OEChem TK - Cheminformatics and 3D molecular data handling.
* OEDepict TK - Elegant 2D structure rendering of compounds.
* OEDocking TK - Docking and scoring.
* Grapheme TK - Advanced structure rendering of compounds.
* GraphSim TK - 2D molecular fingerprints and similarity calculations.
* Lexichem TK - State-of-the-art compound name and structure interconversion with support for multiple languages.
* MolProp TK - 2D molecular property calculation and filtering.
* QuacPac TK - Tautomer generation.
* Omega TK - Conformer generation.
* Shape TK - Molecular shape comparisons based on 3D overlays.
* Spicoli TK - Rapid molecular surface generation and manipulation.
* Szmap TK - Water interactions in the binding site.
* Szykbi TK - Generalized function optimization, e.g. molecular structure optimization.
* Zap TK - An efficient
Poisson-Boltzmann electrostatics
Electrostatics is a branch of physics that studies electric charges at rest (static electricity).
Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amber ...
solver.
See also
*
Computational chemistry
Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of m ...
References
*
*
*
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