High-throughput virtual molecular docking: Hadoop implementation of AutoDock4 on a private cloud

Authors:
Sally R. Ellingson;Jerome Baudry
Affiliations:
University of Tennessee and Oak Ridge National Laboratory, Knoxville, TN, USA;University of Tennessee and Oak Ridge National Laboratory, Knoxville, TN, USA
Venue:
Proceedings of the second international workshop on Emerging computational methods for the life sciences
Year:
2011

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Abstract

Virtual molecular docking is a computational method used in computer-aided drug discovery that calculates the binding affinity of a small molecule drug candidate to a target protein and greatly reduces the time and cost of suggesting new potential pharmaceuticals. This high-throughput screening is a task parallel process and therefore well suited for distributed computing. In this study, we use the open source Hadoop framework implementing the MapReduce paradigm for distributed computing on a cloud platform and the widely used molecular docking program AutoDock. Our high-throughput virtual docking implementation, AutoDockCloud, showed a speed-up of 450 on Kandinsky, a cloud computer located at Oak Ridge National Laboratory.