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J Comput Chem. 2009 Dec;30(16):2785-91. doi: 10.1002/jcc.21256.

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.

Author information

  • 1Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Abstract

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 sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique.

(c) 2009 Wiley Periodicals, Inc.

PMID:
19399780
[PubMed - indexed for MEDLINE]
PMCID:
PMC2760638
Free PMC Article

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