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A Differential Evolution Approach for Protein Folding Using a Lattice Model 被引量:1

A Differential Evolution Approach for Protein Folding Using a Lattice Model
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摘要 Protein folding is a relevant computational problem in Bioinformatics, for which many heuristic algorithms have been proposed. This work presents a methodology for the application of differential evolution (DE) to the problem of protein folding, using the bi-dimensional hydrophobic-polar model. DE is a relatively recent evolutionary algorithm, and has been used successfully in several engineering optimization problems, usually with continuous variables. We introduce the concept of genotype-phenotype mapping in DE in order to provide a mapping between the real-valued vector and an actual folding. The methodology is detailed and several experiments with benchmarks are done. We compared the results with other similar implementations. The proposed DE has shown to be competitive, statistically consistent and very promising. Protein folding is a relevant computational problem in Bioinformatics, for which many heuristic algorithms have been proposed. This work presents a methodology for the application of differential evolution (DE) to the problem of protein folding, using the bi-dimensional hydrophobic-polar model. DE is a relatively recent evolutionary algorithm, and has been used successfully in several engineering optimization problems, usually with continuous variables. We introduce the concept of genotype-phenotype mapping in DE in order to provide a mapping between the real-valued vector and an actual folding. The methodology is detailed and several experiments with benchmarks are done. We compared the results with other similar implementations. The proposed DE has shown to be competitive, statistically consistent and very promising.
出处 《Journal of Computer Science & Technology》 SCIE EI CSCD 2007年第6期904-908,共5页 计算机科学技术学报(英文版)
基金 This work is supported by the Brazilian National Research Council under Grant No.305720/04-0.
关键词 BIOINFORMATICS differential evolution evolutionary computation protein folding bioinformatics, differential evolution, evolutionary computation, protein folding
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  • 1Chikenji G, Kikuchi M, Iba Y. Multi-self-overlap ensemble for protein folding: Ground state search and thermodynamics. Physical Review Letters, 1999, 83(9): 1886-1889.
  • 2Lopes H S, Scapin M P. An enhanced genetic algorithm for protein structure prediction using the 2D hydrophobicpolar model. Lecture Notes in Computer Science, 2005, 3871: 238-246.
  • 3Shmygelska A, Hoos H H. An improved ant colony optimisation algorithm for the 2D HP protein folding problem. Lecture Notes in Computer Science, 2003, 2671: 400-417.
  • 4Dill K A. Theory for the folding and stability of globular proteins. Biochemistry, 1985, 24(6): 1501-1509.
  • 5Crescenzi P, Goldman D, Papadimitriou C et al. On the complexity of protein folding. Journal of Computational Biology, 1998, 5(3): 423-465.
  • 6Li H, Helling R, Tang C et al. Emergence of preferred structures in a simple model of protein folding. Science, 1996, 273(5275): 666-669.
  • 7storn R M, Price K V. Differential evolution - A simple and efficient heuristic for global optimization over continuous spaces. Journal of Global Optimization, 1997, 11(4): 341-359.
  • 8Coelho L S, Lopes H S. Supply chain optimization using chaotic differential evolution method. In Proc. IEEE Systems, Man and Cybernetics Conference, Piscataway, N J, 2006, IEEE Press, pp.3114-3119.
  • 9Yang J, Wongsa S, Kadirkmanathan V et al. Differential evolution and its application to metabolic flux analysis. Lecture Notes in Computer Science, 2005, 3449: 115-124.
  • 10Price K V, Storn R M, Lampinen J A. Differential Evolution - A Practical Approach to Global Optimization. Berlin: Springer-Verlag, 2005.

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