Solving Lattice Protein Folding Problems by Discrete Particle Swarm Optimization

Abstract

Using computer programs to predict protein structures from a mass of protein sequences is promising for discovering the relationship between the protein construction and their functions. In the area of computational protein structure analysis, the hydrophobic-polar (HP) model is one of the most commonly applied models. The protein folding problem based on HP model has been shown as NP-hard, to handle such an NP-hard problem, this paper proposes a discrete particle swarm optimization algorithm (DPSO HP ) to solve various 2D and 3D HP lattice models-based protein folding problems. The discrete particle swarm optimization method used in DPSO HP is based on the set concept and the possibility theory from a set-based PSO (S-PSO). A selection strategy incorporating heuristic information and possibilities is adopted in DPSO HP . A particle’s positions in the algorithm are defined as a set of elements and the velocities of a particle are defined as a set of elements associated with possibilities. The experimental results on a series of 2D and 3D protein sequences show that DPSO HP is promising and performs better than various competitive state-of-the-art evolutionary algorithms.