Algoritmo genético aplicado à predição da estrutura de proteínas utilizando o modelo 3D-HP Side Chain
Resumo
Este trabalho apresenta um algoritmo genético paralelo (AGP) para o problema de dobramento de proteínas, utilizando o modelo 3DHPSC. Este modelo tem sido pouco abordado devido ao elevado grau de complexidade envolvido. Foi proposta uma função de fitness baseada na energia livre e na compacidade do dobramento. Devido a não existir, até então, benchmarks para teste deste modelo, foi proposto um conjunto de 5 sequências baseado em outro modelo mais simplificado. O AGP obteve dobramentos biologicamente coerentes, sugerindo a adequabilidade da metodologia proposta. Trabalhos futuros incluirão a proposição de operadores genéticos baseados em conhecimento, bem como a expansão do benchmark.
Palavras-chave:
Algoritmos genéticos, Bioinformática, Dobramento de proteínas, 3DHP-SC
Referências
Armstrong Junior, N., Lopes, H., and Lima, C. (2007). Reconfigurable computing for accelerating protein folding simulations. Lecture Notes in Computer Science, 4419:314–325.
Berger, B. and Leighton, F. (1998). Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. Journal of Computational Biology, 5(1):27–40.
Cantú-Paz, E. (2000). Efficient and Accurate Parallel Genetic Algorithms. Springer.
Dill, K. (1985). Theory for the folding and stability of globular proteins. Biochemistry, 24(6):1501–1509.
Krasnogor, N., Hart, W., Smith, J., and Pelta, D. (1999). “Protein structure prediction with evolutionary algorithms”. In International Genetic and Evolutionary Computation Conference (GECCO), volume 4, pages 1596–1601.
Li, M. S., Klimov, D. K., and Thirumalai, D. (2002). Folding in lattice models with side chains. Computer Physics Communications, 147(1-2):625–628.
Lopes, H. (2008). “Evolutionary algorithms for the protein folding problem: a review and current trends.”. In Smolinski, T., Milanova, M., and Hassanien, A.-E., editors, Applications of Computational Intelligence in Bioinformatics and Biomedicine: Current Trends and Open Problems, volume I, pages 297–315, Heidelberg. Springer-Verlag.
Maruo, M., Lopes, H., and Delgado, M. (2005). Self-adapting evolutionary parameters: encoding aspects for combinatorial optimization problems. Lecture Notes in Computer Science, 3448:154–165.
Michalewicz, Z. (1996). Genetic Algorithms + Data Structures = Evolution Programs. Springer-Verlag, Berlin, 3rd edition.
Scapin, M. and Lopes, H. (2008). “A hybrid genetic algorithm for the protein folding problem using the 2D-HP lattice model.”. In Yang, A., Shan, Y., and Thu, L., editors, Success in Evolutionary Computation, number 92 in Studies in Computational Intelligence, pages 205–224, Heidelberg. Springer-Verlag.
Yue, K. and Dill, K. (1993). Sequence-structure relationships in proteins and co-polymers. Physical Review E., 48(3):2267–2278.
Berger, B. and Leighton, F. (1998). Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. Journal of Computational Biology, 5(1):27–40.
Cantú-Paz, E. (2000). Efficient and Accurate Parallel Genetic Algorithms. Springer.
Dill, K. (1985). Theory for the folding and stability of globular proteins. Biochemistry, 24(6):1501–1509.
Krasnogor, N., Hart, W., Smith, J., and Pelta, D. (1999). “Protein structure prediction with evolutionary algorithms”. In International Genetic and Evolutionary Computation Conference (GECCO), volume 4, pages 1596–1601.
Li, M. S., Klimov, D. K., and Thirumalai, D. (2002). Folding in lattice models with side chains. Computer Physics Communications, 147(1-2):625–628.
Lopes, H. (2008). “Evolutionary algorithms for the protein folding problem: a review and current trends.”. In Smolinski, T., Milanova, M., and Hassanien, A.-E., editors, Applications of Computational Intelligence in Bioinformatics and Biomedicine: Current Trends and Open Problems, volume I, pages 297–315, Heidelberg. Springer-Verlag.
Maruo, M., Lopes, H., and Delgado, M. (2005). Self-adapting evolutionary parameters: encoding aspects for combinatorial optimization problems. Lecture Notes in Computer Science, 3448:154–165.
Michalewicz, Z. (1996). Genetic Algorithms + Data Structures = Evolution Programs. Springer-Verlag, Berlin, 3rd edition.
Scapin, M. and Lopes, H. (2008). “A hybrid genetic algorithm for the protein folding problem using the 2D-HP lattice model.”. In Yang, A., Shan, Y., and Thu, L., editors, Success in Evolutionary Computation, number 92 in Studies in Computational Intelligence, pages 205–224, Heidelberg. Springer-Verlag.
Yue, K. and Dill, K. (1993). Sequence-structure relationships in proteins and co-polymers. Physical Review E., 48(3):2267–2278.
Publicado
20/07/2009
Como Citar
BENÍTEZ, César Manuel Vargas; LOPES, Heitor S..
Algoritmo genético aplicado à predição da estrutura de proteínas utilizando o modelo 3D-HP Side Chain. In: ENCONTRO NACIONAL DE INTELIGÊNCIA ARTIFICIAL E COMPUTACIONAL (ENIAC), 7. , 2009, Bento Gonçalves/RS.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2009
.
p. 91-100.
ISSN 2763-9061.
