A Global Minimization Algorithm for Empirical Contact Potential Functions

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 sampling and global minimization algorithm, which is called WL, based on Monte Carlo simulation and simulated annealing. Itcan 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.