The implementation of ant colony optimization algorithm for the study of protein folding problem on graphics processing units
The task of finding the tertiary structure of the protein by its primary amino acid sequence (protein folding problem: PFP) - is a major challenge for structural biology. Unfortunately, even such a crude model as HP-PFP-2, which takes into account only hydrophobic interaction of amino acid residues on a two-dimensional lattice is NP-hard and can be successfully solved only by heuristic methods of global optimization, for example, the ant colony optimization algorithm. This article describres the methods of modification and parallelization of ant colony optimization algorithm for the protein folding problem. It is described in detail the software implementation of parallel ant colony optimization algorithm on the graphics processing units.