A hybrid immune-based system for the protein folding problem

Authors:
Carolina P. De Almeida;Richard A. Gonçalves;Myriam R. Delgado
Affiliations:
Federal Technological University of Paraná, Curitiba, PR, Brazil;Federal Technological University of Paraná, Curitiba, PR, Brazil and Department of Computer Science, UNICENTRO, Guarapuava, PR, Brazil;Federal Technological University of Paraná, Curitiba, PR, Brazil
Venue:
EvoCOP'07 Proceedings of the 7th European conference on Evolutionary computation in combinatorial optimization
Year:
2007

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Abstract

This paper describes hybrid algorithms based on artificial immune systems, fuzzy inference systems and tabu search to solve the Protein Folding Problem (PFP) in the 3D Hydrophobic-Polar model, which is a particular instance of the Combinatorial String Folding Problem in a cubic lattice. The proposed methodology aims at enhancing the Clonalg algorithm with a Fuzzy Aging Operator and Weak and Intensive Affinity Maturation. The aging operator uses a fuzzy system to decide which antibodies will be eliminated from the population before the selection stage. The Intensive Maturation employs a Tabu Search strategy. Penalty methods versus feasible search methods are also compared. The proposed hybrid algorithms are tested on a set of standard benchmark instances of PFP and the results attest the efficiency of the methodology.