OpenEye Scientific Software
Encyclopedia
OpenEye Scientific Software develops large-scale molecular modeling applications and toolkits.
and design
, areas of application include structure generation, docking, shape comparison, charge
/electrostatics
, cheminformatics
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.
Other institutions developing software for computational chemistry
Scope
Primarily geared towards drug discoveryDrug discovery
In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which drugs are discovered or designed.In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies or by serendipitous discovery...
and design
Drug design
Drug design, also sometimes referred to as rational drug design or structure-based drug design, is the inventive process of finding new medications based on the knowledge of the biological target...
, areas of application include structure generation, docking, shape comparison, charge
Charge (physics)
In physics, a charge may refer to one of many different quantities, such as the electric charge in electromagnetism or the color charge in quantum chromodynamics. Charges are associated with conserved quantum numbers.-Formal definition:...
/electrostatics
Electrostatics
Electrostatics is the branch of physics that deals with the phenomena and properties of stationary or slow-moving electric charges....
, cheminformatics
Cheminformatics
Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery...
and visualization. The software is designed for scientific rigor, as well as speed, scalability and platform independence
Platform (computing)
A computing platform includes some sort of hardware architecture and a software framework , where the combination allows software, particularly application software, to run...
.
OpenEye makes much of its technology available as toolkits suitable for custom development.
Application Software
- AFITT - Crystallographic refinement and analysis.
- BROOD - BioisostereBioisostereIn medicinal chemistry, bioisosteres are substituents or groups with similar physical or chemical properties which produce broadly similar biological properties to a chemical compound. In drug design, the purpose of exchanging one bioisostere for another is to enhance the desired biological or...
identification using shape, chemistry and electrostatic similarityElectrostaticsElectrostatics is the branch of physics that deals with the phenomena and properties of stationary or slow-moving electric charges....
. - EON - ChemicalChemical substanceIn chemistry, a chemical substance is a form of matter that has constant chemical composition and characteristic properties. It cannot be separated into components by physical separation methods, i.e. without breaking chemical bonds. They can be solids, liquids or gases.Chemical substances are...
similarity analysis via comparison of electrostatics overlayElectrostaticsElectrostatics is the branch of physics that deals with the phenomena and properties of stationary or slow-moving electric charges....
. - FILTER - MolecularMoleculeA molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
screening and selection based on physical property or functional group. - FRED - Extremely fast, systematic docking search for ligand bindingLigandIn coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
within a protein active site. - OMEGA - Systematic high-throughput conformer generation, including 1D or 2D to 3D structure generation.
- QUACPAC - Quality charge states and charges for small molecules and proteins.
- ROCS - Chemical similarityChemical substanceIn chemistry, a chemical substance is a form of matter that has constant chemical composition and characteristic properties. It cannot be separated into components by physical separation methods, i.e. without breaking chemical bonds. They can be solids, liquids or gases.Chemical substances are...
analysis via rapid 3D molecular shape searches. - SZYBKI - Fast structure optimization of ligands in gas-phase, solutionSolutionIn chemistry, a solution is a homogeneous mixture composed of only one phase. In such a mixture, a solute is dissolved in another substance, known as a solvent. The solvent does the dissolving.- Types of solutions :...
, or within a protein active site. - VIDA - Graphical user interface that visualizes, analyzes and manages corporate collections of molecular structures and information.
- VIVANT - Live molecular visualization inside of PowerPoint and web browsers.
Toolkits
Programming libraries providing other applications with object-oriented accessibility to a given set of capabilities.- OEChem TK - Cheminformatics and 3D molecular data handling.
- SCUT Monkeys - All the apps that are included with OEChem.
- GraphSim TK - 2D molecular fingerprints and similarity calculations.
- MolProp TK - 2D molecular property calculation and filtering.
- Lexichem TK - State-of-the-art compound name and structure interconversion with support for multiple languages.
- Ogham TK - Elegant 2D structure rendering of compounds.
- Omega TK - Conformer generation.
- Shape TK - Molecular shape comparisons based on 3D overlays.
- Spicoli TK - Rapid molecular surface generation and manipulation.
- Syzkbi TK - Generalized function optimization, e.g. molecular structure optimization.
- Zap TK - An efficient Poisson-Boltzmann electrostaticsElectrostaticsElectrostatics is the branch of physics that deals with the phenomena and properties of stationary or slow-moving electric charges....
solver.
Other institutions developing software for computational chemistryComputational chemistryComputational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids...
- AccelrysAccelrysAccelrys is a software company headquartered in the US, with representation in Europe and Japan. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries.Accelrys started in 2001...
- Inte:LigandInte:LigandInte:Ligand is a software company headquartered in Vienna, Austria. It provides software and services for chemical research, especially in the areas of drug discovery....
- Chemical Computing GroupChemical Computing GroupChemical Computing Group is a software company specializing in research software for computational chemistry, bioinformatics, cheminformatics, docking, pharmacophore searching and molecular simulation. The company's main customer base consists of pharmaceutical and biotechnology companies, as well...
- VLifeMDS Software
See also
- Anthony NichollsAnthony Nicholls (chemist)Anthony Nicholls is a physicist and entrepreneur from Plymouth, England.-Education:Nicholls first studied Physics at Oxford before joining the Institute for Molecular Biophysics at Florida State University. There he studied quantum dispersion of excitations in biological systems with William...
- Molecular modellingMolecular modellingMolecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...
- CheminformaticsCheminformaticsCheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery...
- Computational chemistryComputational chemistryComputational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids...