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DOVIS: an implementation for high-throughput virtual screening using AutoDock

Shuxing Zhang12, Kamal Kumar1, Xiaohui Jiang1, Anders Wallqvist1 and Jaques Reifman1*

Author Affiliations

1 Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA

2 Department of Experimental Therapeutics, MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 36, Houston, TX 77030, USA

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BMC Bioinformatics 2008, 9:126  doi:10.1186/1471-2105-9-126

Published: 27 February 2008

Abstract

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.