Tackling the Multiple-Minima Problem in Protein Folding by Monte Carlo Simulated Annealing and Generalized-Ensemble Algorithms

Monte Carlo simulations based on simulated annealing and multicanonical algorithm have been performed to predict the secondary and tertiary structures of oligopeptide systems. Two oligopeptides, C-peptide of ribonuclease A and the fragment BPTI(16-36) of bovine pancreatic trypsin inhibitor, were studied. Only the amino-acid sequence information was used as input and initial conformations were randomly generated. The lowest-energy conformations obtained have α-helix structure and β-sheet structure for C-peptide and BPTI(16-36), respectively, in remarkable agreement with experimental results.