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Virtual Laboratory: Enabling On-Demand Drug Design with the World Wide Grid

Rajkumar Buyya·Kim Branson·Jon Giddy·David Abramson
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Abstract

Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the creation of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on distributed resources. It involves screening millions of molecules of chemical compounds against a protein target, chemical database (CDB) to identify those with potential use for drug design. We have grid-enabled the molecular docking process by composing it as a parameter sweep application using the Nimrod-G tools. We then developed new tools for remote access to molecules in CDB small molecule database. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of jobs on distributed grid resources. The results demonstrate the ease of use and suitability of the Nimrod-G and virtual laboratory tools.

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Rajkumar Buyya, Kim Branson, Jon Giddy, David Abramson. 2001-11-17. Virtual Laboratory: Enabling On-Demand Drug Design with the World Wide Grid. https://arxiv.org/abs/cs/0111047

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