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2D ligand |
Overview
Better known as "cheminformatics", the connection information described by bonds forms the fundamentals of chemical synthesis and legality. We discovered how important cheminformatics is the hard way, i.e. we wrote one system then had to start over and write another! The first still forms the basis of an open source project (OELib), the second has become known as OEChem and is the foundation layer for all our software, as well as being a product in of itself.
Products
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OEChem: A cheminformatics tool for modelers. Handles many file formats as flawlessly as any system on earth, allows complete chemical handling, transformation, searching, perception and normalization. Fast, C++ based with Python and Java wrappers, OEChem is the OpenEye infrastructure built to encompass all of our lofty goals (and those of others, such as the PubChem project).
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OMEGA: The bridgehead between 2D representations and 3D, OMEGA is the best conformation generator available. Equally proficient from a 2D format (SMILES, SDF) or a 3D form, OMEGA can rapidly evaluate all energetically feasible structures and return conformations likely to be bioactive (99% accurate to within 2.0 Angstroms in an independent test).
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FILTER: Need to evaluate properties for a large set of compounds? Need to weed out molecules with undesirable properties from a corporate or vendor collection? FILTER is designed around OEChem to rapidly triage chemical collections based on user supplied information and preferences.
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SMACK: Search languages are designed for ease of expression, not efficiency. SMACK used proprietary algorithms to rewrite queries, such as SMARTS or SLN, into forms that may be more readily de constructed by search algorithms found in typical database chemical cartridges.
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Lexichem and Ogham: Applications and toolkits for the parsing of chemical names and the depiction of chemical structures. Lexichem will take structural descriptions and produce IUPAC names and other variations, and then will take names and produce structures. Ogham will produce 2D diagrams from many formats, either in pictorial format or coordinate descriptions.
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VIDA II: Many of our tools either generate or sift through vast quantities of 3D ligand information, and as such VIDA II is the best program available for large scale visualization. VIDA II can handle small lists of molecules or corporate collections and can view them as multi-pane 3D, 2D depictions, SMILES strings, spreadsheet entries, html forms, graphs and drill-down lists. It can view them in the context of proteins or other small molecules, as simple line models or photo-realistic balls and sticks. With a python core VIDA II is easily scriptable and can be tailored to many end-uses. Works, naturally, on many platforms.
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Ligand products
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