A parallel genetic algorithm for protein folding prediction using the 3D-HP side chain model

2009 IEEE Congress on Evolutionary Computation, CEC 2009

Volumn , Issue , 2009, Pages 1297-1304

  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; FITNESS FUNCTIONS; HIGHER-DEGREE; MASTER-SLAVE; PARALLEL GENETIC ALGORITHMS; PARALLEL IMPLEMENTATIONS; PROTEIN FOLDING PREDICTIONS; RUNNING PARAMETERS; SIDE CHAINS; SYNTHETIC SEQUENCE;

BIOINFORMATICS; COMPUTATIONAL EFFICIENCY; DIFFERENTIAL AMPLIFIERS; FUNCTION EVALUATION; GENETIC ALGORITHMS; PARALLEL ALGORITHMS; PROGRAMMED CONTROL SYSTEMS; PROTEIN FOLDING; THREE DIMENSIONAL;

THREE DIMENSIONAL COMPUTER GRAPHICS;

EID: 70449953953     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.2009.4983094     Document Type: Conference Paper

References (19)

1. H. Alba. Parallel Metaheuristics: A New Class of Algorithms. Wiley-Interscience, 2005.
2. J. Atkins and W.E. Hart. On the intractability of protein folding wit a finite alphabet of amino acids. Algorithmics 25, 25: 279-294, 1999.
3. Erick Cantú-paz. A survey of parallel genetic algorithms. Calculateurs Paralleles, pages 611-615, 1998.
4. F.L. Custódio, H.J.C. Barbosa, and L.E. Dardenne. Investigation of the three-dimensional lattice HP protein folding model using a genetic algorithm. Genetics and Molecular Biology, 27: 611-615, 2004.
5. K.A. Dill. Theory for the folding and stability of globular proteins. Biochemistry, 24(6): 1501-1509, 1985.
6. K.A. Dill, S. Bromberg, K. Yue, K.M. Fiebig, D.P. Yee, P.D. Thomas, and H.S. Chan. Principles of protein folding - a perspective from simple exact models. In Protein Science, 1995.
7. D.E. Goldberg. Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley, Reading, MA, 1989.
8. Yu-Zhen Guo and En-Min Feng. The simulation of the threedimensional lattice hydrophobic-polar protein folding. The Journal of Chemical Physics, 125: 234703, 2006.
9. J. H. Holland. Adaptation in natural and artificial systems. MIT Press, 1992.
10. N.B. Armstrong Junior, H.S. Lopes, and C.R.E. Lima. Reconfigurable computing for accelerating protein folding simulations. Lecture Notes in Computer Science, 4419: 314-325, 2007.
11. N. Krasnogor, W.E. Hart, J. Smith, and D.A. Pelta. Protein structure prediction with evolutionary algorithms. In International Genetic and Evolutionary Computation Conference (GECCO), pages 1596-1601, 1999.
12. Mai Suan Li, D. K. Klimov, and D. Thirumalai. Folding in lattice models with side chains. Computer Physics Communications, 147(1): 625-628, 2002.
13. H.S. Lopes. Evolutionary algorithms for the protein folding problem: a review and current trends. In Applications of Computational Intelligence in Bioinformatics and Biomedicine: Current Trends and Open Problems, volume I, Heidelberg, 2008. Springer-Verlag.
14. M.H. Maruo, H.S. Lopes, and M.R.B Delgado. Self-adapting evolutionary parameters: encoding aspects for combinatorial optimization problems. Lecture Notes in Computer Science, 3448: 154-165, 2005.
15. M. Matsumoto and T. Nishimura. Mersenne twister: A 623- dimensionally equidistributed uniform pseudo-random number generator. ACM Transactions on Modeling and Computer Simulation, 8(1): 3-30, 1998.
16. A.L. Patton, W.F. Punch III, and E.D. Goodman. A standard ga approach to native protein conformation prediction. Proceedings of the 6th International Conference on Genetic Algorithms, 1995.
17. S.H. Roosta. Parallel Processing and Parallel Algorithms: Theory and Computation. Springer-Verlag, New York, NJ, 1999.
18. M.P. Scapin and H.S. Lopes. A hybrid genetic algorithm for the protein folding problem using the 2D-HP lattice model. In Success in Evolutionary Computation, pages 205-224, Heidelberg, 2007. Springer-Verlag.
19. R. Unger and J. Moult. A genetic algorithm for 3D protein folding simulations. Proceedings of the Fitfth Annual International Conference on Genetic Algorithms, pages 581-588, 1993.