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

An IBM Redpaper publication

Published 16 April 2008

cover image

IBM Form #: REDP-4410-00
(12 pages)

Authors: P. Therese Lang, Marcus E. Lundberg, Amanda Peters, Carlos P. Sosa


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.

Table of contents

Software and hardware overview
Massively parallel version
Performance results

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