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

Autor: Kin Meng Wong, Hio Kuan Tai, Shirley W. I. Siu
Rok vydání: 2020
Předmět:
Zdroj: Chemical Biology & Drug Design
ISSN: 1747-0285
1747-0277
DOI: 10.1111/cbdd.13764
Popis: 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.
Developed a first grey wolf optimizer based on autodock vina implementation (gwovina) for rigid and flexible‐receptor docking. Enhanced with random walk and rotamer library for side‐chain flexibility. Achieved significant speedup of 2‐ to 7‐fold compared to Vina, and 40‐ to 100‐fold compared to AutoDockFR. GWO has potential usefulness for robust searches in molecular conformational space
Databáze: OpenAIRE
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