基于粒子群算法的骨性关节炎药物分子对接方法应用研究

Application research on osteoarthritis medicine molecular docking based on particle swarm algorithm

通过改进分子对接软件AutoDock的构象搜索算法对治疗骨性关节炎的中药分子进行对接研究.简要分析分子对接方法的基本原理,建立分子对接数学模型,介绍AutoDock半经验结合自由能评分函数;将粒子群算法与自适应局部搜索策略相结合改进了分子对接构象搜索过程;以福建中医大学提供的治疗骨性关节炎的中药分子实验数据为基础,完成了此算法与拉马克遗传算法、遗传算法以及本课题组使用的蚁群算法在最低能量值、对接精度以及对接耗时上的比较实验.实验结果验证了粒子群算法应用在对接构象搜索上的有效性.

The paper is to improve the conformational search algorithm of the AutoDock which is one of the most molecular docking software, to make a docking research about the Chinese medicine molecular that treats the osteoarthritis. The paper describes the basic principles of molecular docking method, establishes the mathematical model of molecular docking, introduces the half experience combined free energy function of AutoDock, then combines the particle swarm algorithm with adaptive local search strategy to improve the optimization process. Based on the experimental data of osteoarthritis Chinese medicine molecular provided by Fujian University of Traditional Chinese Medicine, the paper compares the algorithm with the Lamarckian genetic algorithm, the genetic algorithm, and the ant colony algorithm used in the research group about the lowest energy value, the docking accuracy and doc- king time, results show that the particle swarm algorithm is effective in docking conformational search.