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. 2008 Feb 27;9:126.
doi: 10.1186/1471-2105-9-126.

DOVIS: An Implementation for High-Throughput Virtual Screening Using AutoDock

Free PMC article

DOVIS: An Implementation for High-Throughput Virtual Screening Using AutoDock

Shuxing Zhang et al. BMC Bioinformatics. .
Free PMC article


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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    1. Ghosh S, Nie AH, An J, Huang Z. Structure-based virtual screening for drug discovery. Curr Opin Chem Biol. 2006;10:194–202. doi: 10.1016/j.cbpa.2006.04.002. - DOI - PubMed
    1. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47:1739–49. doi: 10.1021/jm0306430. - DOI - PubMed
    1. Venkatachalam CM, Jiang X, Oldfield T, Waldman M. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model. 2003;21:289–307. doi: 10.1016/S1093-3263(02)00164-X. - DOI - PubMed
    1. Rarey M, Kramer B, Lengauer T. Time-efficient docking of flexible ligands into active sites of proteins. Proc Int Conf Intell Syst Mol Biol. 1995;3:300–8. - PubMed
    1. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem. 1998;19:1639–1662. doi: 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B. - DOI

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