Protein folding simulations and structure predictions Original Research Article

In complex systems such as spin glasses and proteins, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the simulated annealing method and generalized-ensemble algorithms in order to overcome this multiple-minima problem. Besides simulated annealing, three well-known generalized-ensemble algorithms, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described. We then present three new generalized-ensemble algorithms based on the combinations of the three methods.