A GPU-Based Hybrid jDE Algorithm Applied to the 2D-AB Protein Structure Prediction Problem
Mateus Boiani, Gabriel Dominico, Rafael Stubs Parpinelli · 2019
Protein Structure Prediction (PSP) problem is an open problem in bioinformatics and, as the problem scales, complexity and processing time increases. In this way, robust methods and massively parallel architectures are required. This paper presents a GPU-based hybrid algorithm, named cuHjDE, to handle the 2D-AB off-lattice PSP problem. The cuHjDE is composed of the jDE algorithm and the Hooke-Jeeves local search algorithm. An important feature present in the cuHjDE algorithm is the use of a crowding mechanism to avoid premature convergence promoting diversification in the search space. The proposed algorithm is compared with four state-of-the-art algorithms in both artificial and real proteins. Also, the impact of using GPU is analyzed. Experimental results point out that the proposed approach is competitive in artificial sequences and achieved new best results for all real sequence proteins.