GROCK: high-throughput docking using LCG grid tools

Abstract

The study of interactions of proteins with other molecules is a major task to understand living organisms and design new drugs. GROCK is a portal that facilitates mass screening of potential molecular interactions in the life sciences. The main purpose for developing GROCK has been to facilitate users the performance of huge amounts of computational tasks using the power of the grid. In GROCK we have considered issues of high availability, redundancy, failure recovery and maximal exploitation of available grid resources. After trying various approaches we have settled for LCG-submitter, a tool developed for the physics LHC project to solve some of our goals. In this paper we introduce GROCK and analyze its design goals, the challenges found and the solutions we came up with to overcome them.