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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).

SUBMITTER: Bianco G

PROVIDER: S-EPMC4815316 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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

Bianco Giulia G Forli Stefano S Goodsell David S DS Olson Arthur J AJ

Protein science : a publication of the Protein Society 20150707 1

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 w ...[more]

PMID: 26103917

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