An evolutionary approach for protein contact map prediction

Abstract

In this study, we present a residue-residue contact prediction approach based on evolutionary computation. Some amino acid properties are employed according to their importance in the folding process: hydrophobicity, polarity, charge and residue size. Our evolutionary algorithm provides a set of rules which determine different cases where two amino acids are in contact. A rule represents two windows of three amino acids. Each amino acid is characterized by these four properties. We also include a statistical study for the propensities of contacts between each pair of amino acids, according to their types, hydrophobicity and polarity. Different experiments were also performed to determine the best selection of properties for the structure prediction among the cited properties. © 2011 Springer-Verlag.