Parallelism, hybridism and coevolution in a multi-level ABC-GA approach for the protein structure prediction problem

Authors:
César Manuel Vargas Benitez;Rafael Stubs Parpinelli;Heitor Silvério Lopes
Affiliations:
Bioinformatics Laboratory, Federal University of Technology Paraná (UTFPR), Curitiba, (PR)80230-901, Brazil;Bioinformatics Laboratory, Federal University of Technology Paraná (UTFPR), Curitiba, (PR)80230-901, Brazil and Applied Cognitive Computing Group, Santa Catarina State University (UDESC), J ...;Bioinformatics Laboratory, Federal University of Technology Paraná (UTFPR), Curitiba, (PR)80230-901, Brazil
Venue:
Concurrency and Computation: Practice & Experience
Year:
2012

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Abstract

This paper reports the hybridization of the artificial bee colony (ABC) and a genetic algorithm (GA), in a hierarchical topology, a step ahead of a previous work. We used this parallel approach for solving the protein structure prediction problem using the three-dimensional hydrophobic-polar model with side-chains (3DHP-SC). The proposed method was run in a parallel processing environment (Beowulf cluster), and several aspects of the modeling and implementation are presented and discussed. The performance of the hybrid-hierarchical ABC-GA approach was compared with a hybrid-hierarchical ABC-only approach for four benchmark instances. Results show that the hybridization of the ABC with the GA improves the quality of solutions caused by the coevolution effect between them and their search behavior. Copyright © 2011 John Wiley & Sons, Ltd.