A Global Minimization Algorithm for Empirical Contact Potential Functions

作     者：WANGYu-hong LIWei 

作者机构：CollegeofLifeScienceJilinUniversityChangchun130023P.R.China 

出 版 物：《Chemical Research in Chinese Universities》 (高等学校化学研究（英文版）)

年 卷 期：2004年第20卷第5期

页      面：572-574页

核心收录：

学科分类：081704[工学-应用化学] 07[理学] 070304[理学-物理化学(含∶化学物理)] 08[工学] 0817[工学-化学工程与技术] 070303[理学-有机化学] 0703[理学-化学] 

基　　金：Supported by the National Natural Science Foundation of China(No.30 2 4 0 0 16) 

主　　题：Global minimization Contact potential function Simulated annealing Monte Carlo simulation 

摘      要：Global minimization algorithm is indispensable to solving the protein folding problem based upon thermodynamic hypothesis. Here we propose a pseudo potential function, contact difference(CD), for simulating empirical contact potential functions and testing global minimization algorithm. The present paper covers conformational sampling and global minimization algorithm called BML03, based upon Monte Carlo and simulated annealing, which is able to locate CD′s global minimum and refold extended protein structures into ones with root mean square distance(RMSD) as small as 0.03 nm from the native structures. For empirical contact potential functions, these results demonstrate that their global minimization problems may be solvable.