Protein Folding Based on Simulated Annealing Algorithm

Protein folding problem is one of the most important problems in bioinformatics, and hydrophobic polar model is a wide abstract model in study of this problem. Simulated annealing is a heuristic global optimization algorithm, which has been successfully applied to many difficult optimization problems. This paper proposes an improved simulated annealing algorithm to search the ground state of HP lattice model for protein folding. Numerical results show that the improved simulated annealing algorithm can find the known lowest ground state faster for the given HP sequences in simple lattice model.