Protein Folding Simulations by Simulated Annealing and Generalized-Ensemble Algorithms

Monte Carlo simulated annealing and generalized-ensemble algorithms for protein fold-ing problem are described in detail. Two oligopeptides, Met-enkephalin and C-peptide of ribonuclease A were studied. Only the amino-acid sequence information was used as input and initial conformations were randomly generated. The lowest-energy conformation ob-tained for C-peptide has an α-helix structure in remarkable agreement with experimental results. In protein and other complex systems, simulations at low temperatures tend to get trapped in a few of huge number of local-minimum-energy states. One way to overcome this multiple-minima problem is by Monte Carlo simulated annealing, 1) which is perhaps the most widely used optimization method. Another effective way i