Combination of genetic crossover and replica-exchange method for conformational search of protein systems

Abstract

We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global conformational space by exchanging the corresponding parts between a pair of conformations of a protein. In this study, we applied this method to an $\alpha$-helical protein, Trp-cage mini protein, which has 20 amino-acid residues. The conformations obtained from the simulations are in good agreement with the experimental results.