Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking

Boxin Guan, Changsheng Zhang, Jiaxu Ning
2017 AMB Express  
Protein-ligand docking plays an important role in computer-aided pharmaceutical development. Protein-ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to improve an efficient algorithm has become a very significant challenge. In this paper, a novel search algorithm based on crossover elitist preservation mechanism (CEP) for solving protein-ligand docking problems
more » ... proposed. The proposed algorithm, namely genetic algorithm with crossover elitist preservation (CEPGA), employ the CEP to keep the elite individuals of the last generation and make the crossover more efficient and robust. The performance of CEPGA is tested on sixteen molecular docking complexes from RCSB protein data bank. In comparison with GA, LGA and SODOCK in the aspects of lowest energy and highest accuracy, the results of which indicate that the CEPGA is a reliable and successful method for protein-ligand docking problems. which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
doi:10.1186/s13568-017-0476-0 pmid:28905320 pmcid:PMC5597564 fatcat:rwekvveuufeszklqhz73ua2anm