title: Covalent docking using autodock: Two-point attractor and flexible side chain methods.
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).
authors.affiliation: Department of Life and Environmental Sciences, Drug Sciences Section, University of Cagliari, via Ospedale 72, Cagliari, 09124, Italy.
authors.forename: Giulia
authors.initials: G
authors.lastname: Bianco
authors.affiliation: 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.
authors.forename: Stefano
authors.initials: S
authors.lastname: Forli
authors.affiliation: 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.
authors.forename: David S
authors.initials: DS
authors.lastname: Goodsell
authors.affiliation: 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.
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Olson
mesh_terms: D001331:Automation; D008024:Ligands; D062105:Molecular Docking Simulation; D011506:Proteins / Q000737:chemistry*
chemical_list: D008024:Ligands; D011506:Proteins
keywords: computational docking; computer-aided drug design; covalent inhibitors; ligand-protein interactions