The Virtual Laboratory: Enabling Molecular Modeling for Drug Design on the World Wide Grid

Computational Grids are emerging as a new paradigm for sharing and aggregation of geographically distributed resources for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application development, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the development of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on geographically distributed resources. It involves screening millions of compounds in the chemical database (CDB) against a protein target to identify those with potential use for drug design. We have used the Nimrod-G parameter specification language for transforming molecular docking application as a parameter sweep application for executing on distributed systems. We have developed new tools for enabling access to ligand records/molecules in the CDB from remote resources. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of docking jobs on the World-Wide Grid (WWG) resources. The results demonstrate the ease of use and power of the Nimrod-G and virtual laboratory tools for grid computing.