A Global Minimization Algorithm for Empirical Contact Potential Functions  

作　　者：WANG Yu-hong LI Wei 

机构地区：[1]Department of Molecular Biology, College of Life Sciences, Jilin University, Changchun 130021, P. R. China

出　　处：《Chemical Research in Chinese Universities》2006年第2期248-250,共3页高等学校化学研究（英文版）

基　　金：SupportedbytheNationalNaturalScienceFoundationofChina(No.39980005).

摘　　要：Global minimization algorithm is indispensable for solving protein folding problems based on thermodynamic hypothesis. A contact difference （CD） based on pseudo potential function, for simulating empirical contact potential functions and testing global minimization algorithm was proposed. The present article describes a conformational sampiing and global minimization algorithm, which is called WL, based on Monte Carlo simulation and simulated annealing. It can be used to locate CD＇s globe minimum and refold extended protein structures, as small as 0. 03 nm, from the native structures, back to ones with root mean square distance（RMSD）. These results demonstrate that the global minimization problems for empirical contact potential functions may be solvable.Global minimization algorithm is indispensable for solving protein folding problems based on thermodynamic hypothesis. A contact difference （CD） based on pseudo potential function, for simulating empirical contact potential functions and testing global minimization algorithm was proposed. The present article describes a conformational sampiing and global minimization algorithm, which is called WL, based on Monte Carlo simulation and simulated annealing. It can be used to locate CD＇s globe minimum and refold extended protein structures, as small as 0. 03 nm, from the native structures, back to ones with root mean square distance（RMSD）. These results demonstrate that the global minimization problems for empirical contact potential functions may be solvable.

关 键 词：Global minimization Contact potential function Simulated annealing Monte Carlo simulation 

分 类 号：Q51[生物学—生物化学]