Hierarchical parallel genetic algorithm applied to the three-dimensional HP side-chain protein folding problem

Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics

Volumn , Issue , 2010, Pages 2669-2676

  Benítez, César Manuel Vargas ^a   Lopes, Heitor Silvério ^a  

^a UNIVERSIDADE TECNOLÓGICA FEDERAL DO PARANÁ   (Brazil)

Author keywords

3DHP SC; Bioinformatics; Genetic algorithm; Protein folding

Indexed keywords

3DHP-SC; PARALLEL GENETIC ALGORITHMS; PROTEIN FOLDING PROBLEM; SIDE-CHAIN;

BIOINFORMATICS; CYBERNETICS; PROTEIN FOLDING;

GENETIC ALGORITHMS;

EID: 78751519354     PISSN: 1062922X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICSMC.2010.5641895     Document Type: Conference Paper

References (25)

1. C.B. Anfinsen. Principles that govern the folding of protein chains. Science, (181), 1973.
2. J. Atkins and W.E. Hart. On the intractability of protein folding with a finite alphabet. Algorithmica, 25(2-3):279-294, 1999.
3. C.M.V. Benítez and H.S. Lopes. A parallel genetic algorithm for protein folding prediction using the 3DHP side-chain model. In Proc. IEEE Congr. on Evolutionary Computation, pages 1297-1304, Piscataway, USA, 2009.
4. C.M.V. Benítez and H.S. Lopes. Protein structure prediction with the 3D-HP side-chain model using a master-slave parallel genetic algorithm. Journal of the Brazilian Computer Society, 16:69-78, 2010.
5. H.M. Berman, J. Westbrook, Z. Feng, and G. Gilliland et al. UniProt archive. Nucleic Acids Research, 28(1):235-242, 2000.
6. th Conf. North American Transputer Users Group on Transputer Research and Applications (NATUG-6), pages 67-82, 1993.
7. E. Cantú-Paz. Efficient and Accurate Parallel Genetic Algorithms. Springer, New York, USA, 2000.
8. The UniProt Consortium. The universal protein resource (UniProt) 2009. Nucleic Acids Research, 37:D169-D174, 2009.
9. K.A. Dill, S. Bromberg, K. Yue, and K.M. Fiebig et al. Principles of protein folding - a perspective from simple exact models. Protein Science, 4(4):561-602, 1995.
10. M. Dorigo and T. Stützle. Ant Colony Optimization. MIT Press, Cambridge, MA, USA, 2004.
11. F. Hembecker, H.S. Lopes, and W. Godoy Jr. Particle swarm optimization for the multidimensional knapsack problem. Lecture Notes in Computer Science, 4331:358-365, 2007.
12. D. Karaboga. An idea based on honey bee swarm for numerical optimization. Technical report, Department Computer Engineering Department, Erciyes University, 2005.
13. J. Kennedy and R. Eberhart. Particle Swarm Optimization. In Proceedings of the IEEE International Conference on Neural Networks, volume 4, pages 1942-1948, Piscataway, NJ, USA, 1995. IEEE Computer Society.
14. N. Krasnogor, W.E. Hart, J. Smith, and D.A. Pelta. Protein structure prediction with evolutionary algorithms. In Proc. Genetic and Evolutionary Computation Conf., pages 1596-1601, 1999.
15. M.S. Li, D.K. Klimov, and D. Thirumalai. Folding in lattice models with side chains. Computer Physics Communications, 147(1):625-628, 2002.
16. H.S. Lopes. Evolutionary algorithms for the protein folding problem: A review and current trends. In Computational Intelligence in Biomedicine and Bioinformatics, volume I, pages 297-315. Springer-Verlag, Heidelberg, 2008.
17. H.S. Lopes and M.P. Scapin. An enhanced genetic algorithm for protein structure prediction using the 2D hydrophobic-polar model. Lecture Notes in Computer Science, 3871:238-246, 2005.
18. th edition, 2008.
19. th Int. Conf. on Genetic Algorithms, pages 574-581, 1995.
20. M.P. Scapin and H.S. Lopes. A hybrid genetic algorithm for the protein folding problem using the 2D-HP lattice model. In A. Yang, Y. Shan, and L.T. Bui, editors, Success in Evolutionary Computation, number 205-224, pages 205-224. Springer, Heidelberg, 2007.
21. C. Thachuk, A. Shmygelska, and H.H. Hoos. A replica exchange Monte Carlo algorithm for protein folding in the HP model. BMC Bioinformatics, 8, 2007.
22. th Ann. Int. Con! on Genetic Algorithms, pages 581-588, 1993.
23. Xin-She Yang. Nature-Inspired Metaheuristic Algorithms. Luniver Press, York, UK, 2008.
24. K. Yue and K.A. Dill. Sequence-structure relationships in proteins and copolymers. Physical Review E, 48(3):2267-2278, 1993.
25. K. Yue, K. Fiebig, and P. Thomas et al. A test of lattice protein folding algorithms. Proceedings of the National Academy of Sciences of USA, V. 91:581-588, 1994