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High-throughput virtual molecular docking with AutoDockCloud

Authors

  • Sally R. Ellingson,

    1. Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
    2. UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
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  • Jerome Baudry

    Corresponding author
    1. UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
    2. Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
    • Correspondence to: Jerome Baudry, Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.

      E-mail: jbaudry@utk.edu

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  • Categories and Subject Descriptors

  • C.2.4 [Distributed Systems]: Distributed Applications; D.1.3 [Programming Techniques]: Concurrent Programming – Distributed programming; I.6.0 [Computing Methodologies]: Simulation and Modeling – General; J.3. [Computer Applications]: Life and Medical Sciences - Biology and genetics, Health, Medical information systems.

  • General Terms

  • Performance, Design

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. High-throughput virtual screenings calculate the binding affinities for a large number of molecules at once and ranks potential drug candidates to 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. The initial implementation of AutoDockCloud showed a speed-up of 450 on Kandinsky, a cloud computer located at Oak Ridge National Laboratory. Further modifications show promise for a greater speed-up of large chemical library screenings and also incorporates and distributes the pre-docking procedures. Copyright © 2012 John Wiley & Sons, Ltd.

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