Abstract: In this paper are reported the local minimum problem by means of current greedy algorithm for training the empirical potential function of protein folding on 8623 non-native structures of 31 globular proteins and a solution of the problem based upon the simulated annealing algorithm.This simulated annealing algorithm is indispensable for developing and testing highly refined empirical potential functions.

Key words: Empirical potential function of protein folding, Training, Simulated annealing, Greedy algorithm