TY - JOUR
T1 - DOVIS
T2 - An implementation for high-throughput virtual screening using AutoDock
AU - Zhang, Shuxing
AU - Kumar, Kamal
AU - Jiang, Xiaohui
AU - Wallqvist, Anders
AU - Reifman, Jaques
N1 - Funding Information:
We would like to thank Drs. M. Lee and M. Olson for helpful suggestions. This work was sponsored by the US Department of Defense High Performance Computing Modernization Program (HPCMP), under the High Performance Computing Software Applications Institutes (HSAI) initiative. The opinions or assertions contained herein are the private views of the authors and are not to be construed as official or as reflecting the views of the US Army or the US Department of Defense. This paper has been approved for public release and distribution is unlimited.
PY - 2008/2/27
Y1 - 2008/2/27
N2 - Background: Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. Results: We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried. Conclusion: DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.
AB - Background: Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. Results: We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried. Conclusion: DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.
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U2 - 10.1186/1471-2105-9-126
DO - 10.1186/1471-2105-9-126
M3 - Article
C2 - 18304355
AN - SCOPUS:40749120187
SN - 1471-2105
VL - 9
JO - BMC bioinformatics
JF - BMC bioinformatics
M1 - 126
ER -