A multi-objective evolutionary algorithm for protein structure prediction with immune operators

Abstract

Genetic algorithms (GA) are often well suited for optimisation problems involving several conflicting objectives. It is more suitable to model the protein structure prediction problem as a multi-objective optimisation problem since the potential energy functions used in the literature to evaluate the conformation of a protein are based on the calculations of two different interaction energies: local (bond atoms) and non-local (non-bond atoms) and experiments have shown that those types of interactions are in conflict, by using the potential energy function, Chemistry at Harvard Macromolecular Mechanics. In this paper, we have modified the immune inspired Pareto archived evolutionary strategy (I-PAES) algorithm and denoted it as MI-PAES. It can effectively exploit some prior knowledge about the hydrophobic interactions, which is one of the most important driving forces in protein folding to make vaccines. The proposed MI-PAES is comparable with other evolutionary algorithms proposed in literature, both in terms of best solution found and the computational time and often results in much better search ability than that of the canonical GA.

Keywords:

• protein structure prediction
• multi-objective evolutionary algorithms
• genetic algorithms
• immune operators
• Pareto archived evolutionary strategy