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GWOVina: A grey wolf optimization approach to rigid and flexible receptor docking.

ABSTRACT: Protein-ligand docking programs are indispensable tools for predicting the binding pose of a ligand to the receptor protein. In this paper, we introduce an efficient flexible docking method, GWOVina, which is a variant of the Vina implementation using the grey wolf optimizer (GWO) and random walk for the global search, and the Dunbrack rotamer library for side-chain sampling. The new method was validated for rigid and flexible-receptor docking using four independent datasets. In rigid docking, GWOVina showed comparable docking performance to Vina in terms of ligand pose RMSD, success rate, and affinity prediction. In flexible-receptor docking, GWOVina has improved success rate compared to Vina and AutoDockFR. It ran 2 to 7 times faster than Vina and 40 to 100 times faster than AutoDockFR. Therefore, GWOVina can play a role in solving the complex flexible-receptor docking cases and is suitable for virtual screening of compound libraries. GWOVina is freely available at https://cbbio.cis.um.edu.mo/software/gwovina for testing.

SUBMITTER: Wong KM

PROVIDER: S-EPMC7818481 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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GWOVina: A grey wolf optimization approach to rigid and flexible receptor docking.

Wong Kin Meng KM Tai Hio Kuan HK Siu Shirley W I SWI

Chemical biology & drug design 20200810 1

Protein-ligand docking programs are indispensable tools for predicting the binding pose of a ligand to the receptor protein. In this paper, we introduce an efficient flexible docking method, GWOVina, which is a variant of the Vina implementation using the grey wolf optimizer (GWO) and random walk for the global search, and the Dunbrack rotamer library for side-chain sampling. The new method was validated for rigid and flexible-receptor docking using four independent datasets. In rigid docking, G ...[more]

PMID: 32679606

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Dataset Information

GWOVina: A grey wolf optimization approach to rigid and flexible receptor docking.

Publications

GWOVina: A grey wolf optimization approach to rigid and flexible receptor docking.

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