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Protein Sci. 2016 Jan;25(1):295-301. doi: 10.1002/pro.2733. Epub 2015 Jul 7.

Covalent docking using autodock: Two-point attractor and flexible side chain methods.

Author information

1
Department of Life and Environmental Sciences, Drug Sciences Section, University of Cagliari, via Ospedale 72, Cagliari, 09124, Italy.
2
Molecular Graphics Lab, Department of Integrative Structural and Computational Biology, MB-112, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037-1000.

Abstract

We describe two methods of automated covalent docking using Autodock4: the two-point attractor method and the flexible side chain method. Both methods were applied to a training set of 20 diverse protein-ligand covalent complexes, evaluating their reliability in predicting the crystallographic pose of the ligands. The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested. Both methods are freely available at the AutoDock website (http://autodock.scripps.edu).

KEYWORDS:

computational docking; computer-aided drug design; covalent inhibitors; ligand-protein interactions

PMID:
26103917
PMCID:
PMC4815316
DOI:
10.1002/pro.2733
[Indexed for MEDLINE]
Free PMC Article

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