Abstract: 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.

Key words: Global minimization, Contact potential function, Simulated annealing, Monte Carlo simulation, Global minimization, Contact potential function, Simulated annealing, Monte Carlo simulation