Guan Boxin, Zhang Changsheng, Ning Jiaxu
Key Laboratory of Medical Image Computing of Ministry of Education, Northeastern University, Shenyang, 110819, People's Republic of China.
AMB Express. 2017 Sep 13;7(1):174. doi: 10.1186/s13568-017-0476-0.
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 is 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.
蛋白质-配体对接在计算机辅助药物研发中起着重要作用。蛋白质-配体对接可定义为一种带有评分函数的搜索算法，其目的是确定具有最低能量的配体和受体的构象。因此，改进一种高效算法已成为一项非常重大的挑战。本文提出了一种基于交叉精英保留机制（CEP）的新型搜索算法来解决蛋白质-配体对接问题。所提出的算法，即具有交叉精英保留的遗传算法（CEPGA），采用CEP来保留上一代的精英个体，并使交叉更高效、更稳健。在来自RCSB蛋白质数据库的16个分子对接复合物上测试了CEPGA的性能。在最低能量和最高准确性方面与GA、LGA和SODOCK进行比较，结果表明CEPGA是解决蛋白质-配体对接问题的一种可靠且成功的方法。
