Protein Structure Prediction Using Bee Colony Optimization Metaheuristic

Predicting the native structure of proteins is one of the most challenging problems in molecular biology. The goal is to determine the three-dimensional structure from the one-dimensional amino acid sequence. De novo prediction algorithms seek to do this by developing a representation of the proteins structure, an energy potential and some optimization algorithm that finds the structure with minimal energy. Bee Colony Optimization (BCO) is a relatively new approach to solving optimization problems based on the foraging behaviour of bees. Several variants of BCO have been suggested in the literature. We have devised a new variant that unifies the existing and is much more flexible with respect to replacing the various elements of the BCO. In particular, this applies to the choice of the local search as well as the method for generating scout locations and performing the waggle dance. We apply our BCO method to generate good solutions to the protein structure prediction problem. The results show that BCO generally finds better solutions than simulated annealing which so far has been the metaheuristic of choice for this problem.