Evolutionary Algorithm for Protein Structure Prediction

Abstract

A protein is characterized by its 3D structure,which defines its biological function. In this paper, we present a scatter search algorithm for predicting 3D structures of proteins based on torsion angles representation. Given the protein¿s sequence of amino acids, our algorithm produces a 3D structure that aims to minimize the energy function associated with the structure. Scatter search is an evolutionary approach that is based on a population of candidate solutions. We evaluate our algorithm on proteins taken from a protein data bank. The results show that our algorithm is able to produce 3D structures with good sub-optimal energy values. Also, the root mean square deviations of these structures from the reference proteins are promising within limits imposed by the assumptions made.