High Throughput Computing Validation for Drug Discovery Using the DOCK Program on a Massively Parallel System

TitleHigh Throughput Computing Validation for Drug Discovery Using the DOCK Program on a Massively Parallel System
Publication TypeReport
Year of Publication2007
AuthorsPeters, A, Lundberg, ME, Lang, PT, and Sosa, CP
Series TitleRedPaper
Date Published09/2007
InstitutionIBM
CityArmonk, NY
Abstract

This IBM ® Redpaper publication presents a virtual screening study of the DOCK Version 6.0 molecular docking software package on a massively parallel system, the IBM System Blue Gene ® supercomputer, Blue Gene/L.1 Virtual screening of very large libraries of small ligands requires not only efficient algorithms but an efficient implementation for docking thousands, if not millions, of compounds simultaneously in a reasonable amount of time. This paper presents a series of receptor-ligand docking benchmarks using DOCK Version 6.0 to show performance improvements with better load balancing and file I/O improvements. In addition, a version was implemented to take advantage of the High Throughput Computing (HTC) feature on the Blue Gene supercomputer.