Sulimov A.V., Kutov D.K., Katkova E.V., Sulimov V.B. Application of the docking program SOL for CSAR benchmark // 244th ACS National Meeting, Philadelphia, Pennsylvania, USA, 19-23 August, 2012
Docking program SOL and postprocessing were tested against CSAR Benchmark. Molecules preparation will be described in details. SOL is the original program developed on the base of genetic algorithm, MMFF94 force field, rigid protein energy grid including desolvation in the frame of simplified GB model, VdW and electrostatic interactions and internal strain energy. Important SOL feature is single- or multi-processor performance up to hundreds of cores. This feature gives the opportunity either to screen hundreds of thousand compounds or very fast energy grid generation and ligand docking, e.g. one ligand docking for less than 1 minute at 256 cores. Sol has demonstrated good performance at general type validation tests (www.keenbase.ru) and has been employed for new thrombin inhibitors discovery (PLoS ONE (2011) 6(5) e19969). At CSAR benchmark SOL demonstrates good performance for two target-proteins and bad one for another two proteins. Failures are discussed.
Docking, SOL, CSAR, force field