Generating structure from names
OpenEye Scientific Software has released Ogham and LexiChem, programs that handle 2D rendering, naming of compounds and the generation of structures from names. The company has focused on software for 3D modelling, but, for communication between chemists, names and 2D renderings are extremely important.
Molecular structures have long been depicted by Kekule drawings -- lines between points to represent bonds and atoms. Ogham, named after the ancient Irish pictographic alphabet, renders these 2D Kekule drawings from 3D structures or connectivity information. It offers display controls, such as colour, size, optional use of superatoms, or style of representation for aromatic and dative bonds. Importantly, Ogham provides a consistent and specifiable orientation of core substructures, making it easy to spot common and alternate moieties in a series of compounds.
LexiChem provides efficient conversion from chemical names into chemical structures and vice versa. Compounds can be named in a number of styles including fully systematic, preferred IUPAC 2005, acceptable common-usage IUPAC, CAS naming conventions, and non-IUPAC traditional common names.
Both LexiChem and Ogham are available either as standalone applications or as C++ toolkits for in-house or third-party software development purposes.
The company has also released version 2.1 of FRED, its fast docking program. For every ligand, FRED searches all possible poses within a protein's active site, filtering for shape complementarity and pharmacophoric features before evaluating with several scoring functions (ChemScore, PLP, ScreenScore, ChemGauss, PBSA).
FRED uses a systematic search algorithm, rather than stochastic methods, to predicting binding modes in a reproducible manner. FRED docks about a dozen ligand conformers per second per processor.