Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 30, Issue 16, Pages 2785-2791Publisher
WILEY
DOI: 10.1002/jcc.21256
Keywords
AutoDock; computational docking; protein flexibility; covalent ligands; computer-aided drug design
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Funding
- National Institutes of Health [RO1 GM069832]
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We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible side-chains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based clocking method and a modification of the flexible sidechain technique. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 2785-2791, 2009
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