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