Protein structure prediction with evolutionary algorithms

Abstract

Evolutionary algorithms have been successfully applied to a variety of molecular structure prediction problems. In this paper we reconsider the design of genetic algorithms that have been applied to a simple protein structure prediction problem. Our analysis considers the impact of several algorithmic factors for this problem: the conformational representation, the energy formulation and the way in which infeasible conformations are penalized. Further we empirically evaluate the impact of these factors on a small set of polymer sequences. Our analysis leads to specific recommendations for both GAs as well as other heuristic methods for solving PSP on the HP model. 1 INTRODUCTION A protein is a chain of amino acid residues that folds into a specific native tertiary structure under certain physiological conditions. A protein's structure determines its biological function. Consequently, methods for solving protein structure prediction (PSP) problems are valuable tools for modern molecula...