计算机辅助药物分子对接并行演化设计  

Computer Aided Drug Molecular Docking Design Based on Parallel Evolution

作　　者：李纯莲[1] 王希诚[2] 赵金城[3] 

机构地区：[1]大连理工大学电子与信息工程学院计算机科学与工程系 [2]大连理工大学工业装备结构分析国家重点实验室,大连116023 [3]大连大学生物信息学与分子设计研究所,大连116621

出　　处：《计算机辅助设计与图形学学报》2005年第1期168-173,共6页Journal of Computer-Aided Design & Computer Graphics

基　　金：国家自然科学基金(10272030);国家重点基础研究发展规划项目(19990328)

摘　　要：对分子对接理论作了简单介绍 ,建立了一个基于柔性配体分子与刚性受体分子对接的数学规划模型 ,将分子对接中的构象优化搜索转化为求解约束极小化问题的过程 ,并采用带有空间收缩的多种群并行遗传算法进行求解 在分布式存储的并行机曙光 30 0 0上模拟计算表明 ,该设计具有很高的并行加速比 ,在保证分子对接的准确性和有效性的前提下 。An optimal conformation search approach to the rigid receptor and flexible ligand docking problem is presented. The conformation searching process in molecular docking is modeled as an optimization problem with multiple constraints, and a new iteration scheme in conjunction with multi-population genetic strategy and an entropy-based searching technique is developed to do the conformation optimization. In the proposed GA, the general problem of early premature is avoided by the diversity of populations; taking the precision of contracted variables space as terminate rule makes the algorithm convergent reasonably; the specific strategy of reserving the most fitness member with evolutionary historic information ensures the global solution; the application of micro-population cuts down the calculation complexity. Besides, a parallel computing strategy with coarse grain is also employed on a Tianchao Dawning 3000 parallel computer and a high speedup and efficiency are reached. An application of the proposed method is illustrated.

关 键 词：分子对接 结合位点 遗传算法 信息熵 并行计算 

分 类 号：O631[理学—高分子化学]