Rotation crossover and K-site move mutation for evolutionary protein folding in 3D FCC HP model (preliminary version)

Abstract

In this paper we present a new evolutionary algorithm for the protein folding problem. We study the problem in the 3D FCC HP model which has been widely used in previous research. Our focus is to develop evolutionary algorithms (EA) which are robust, easy to operate and can handle various energy functions. We propose lattice rotation for crossover and K-site move for mutation, which form the key components of our evolutionary algorithms. Experiment shows that our algorithms are able to find minimum-energy conformations for many sequences whose optimal conformations are not found in previous EA-based algorithms. Furthermore, our idea can be easily integrated into Monte Carlo and Tabu searches as approaches for local searches.