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

An IBM Redpaper publication


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


Publish Date
16 April 2008

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