ConfGen: a conformational search method for efficient generation of bioactive conformers.

摘要: We describe the methodology, parametrization, and application of a conformational search method, called ConfGen, designed to efficiently generate bioactive conformers. define efficiency as ability conformation within small total number conformations using reasonable amount computer time. The method combines physics-based force field calculations with empirically derived heuristics achieve efficient searching prioritization ligand’s space. While many parameter settings are supported, four modes spanning range speed quality trades-offs defined characterized. validation set used test is composed ligands from 667 crystal structures covering broad array target ligand classes. With fastest mode, ConfGen uses an average 0.5 s per generates only 14.3 conformers ligand, at least one which lies 2.0 A root-mean-squared deviation structure for 96%...