Anfinsen CB Principles that govern the folding of protein chains. Science (181)
Armstrong NB Jr, Lopes HS, Lima CRE (2007) Reconfigurable computing for accelerating protein folding simulations. Lect Notes Comput Sci 4419:314–325
Article
Google Scholar
Atkins J, Hart WE (1999) On the intractability of protein folding with a finite alphabet. Algorithmica 25(2–3):279–294
Article
MathSciNet
Google Scholar
Benítez CMV, Lopes HS (2009) Algoritmo genético aplicado à predição da estrutura de proteínas utilizando o modelo 3D-HP side chain. In: Anais do VII encontro nacional de inteligência artificial (ENIA)
Benítez CMV, Lopes HS (2009) A parallel genetic algorithm for protein folding prediction using the 3DHP side-chain model. In: Proceedings of IEEE congress on evolutionary computation. IEEE Computer Society, Piscataway, pp 1297–1304
Google Scholar
Berger B, Leighton FT (1998) Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. J Comput Biol 5(1):27–40
Article
Google Scholar
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) UniProt archive. Nucleic Acids Res 28(1):235–242
Article
Google Scholar
Box GE, Hunter WG, Hunter JS (2005) Statistics for experimenters: design, innovation, and discovery, 2nd edn. Wiley, New York
Google Scholar
Cantú-Paz E (2000) Efficient and accurate parallel genetic algorithms. Springer, New York
Google Scholar
Crescenzi P, Goldman D, Papadimitriou C, Piccolboni A, Yannakakis M (1998) On the complexity of protein folding. J Comput Biol 5(3):423–465
Article
Google Scholar
Custódio FL, Barbosa HJC, Dardenne LE (2004) Investigation of the three-dimensional lattice HP protein folding model using a genetic algorithm. Genet Mol Biol 27(4):611–615
Article
Google Scholar
Deb K (2001) Multi-objective optimization using evolutionary algorithms. Wiley, Chichester
Google Scholar
Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS (1995) Principles of protein folding—a perspective from simple exact models. Protein Sci 4(4):561–602
Article
Google Scholar
Gropp W, Lusk E, Thakur R (1999) Using MPI2: advanced features of the message-passing interface. MIT Press, Cambridge
Google Scholar
Hembecker F, Lopes HS, Godoy W Jr (2007) Particle swarm optimization for the multidimensional knapsack problem. Lect Notes Comput Sci 4331:358–365
Article
Google Scholar
Krasnogor N, Hart WE, Smith J, Pelta DA (1999) Protein structure prediction with evolutionary algorithms. In: Banzhaf D, Eiben G, Honovar J, Smith S (eds) Proceedings of the international genetic and evolutionary computation conference, San Mateo, CA, pp 1596–1601
Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R (2004) UniProt archive. Bioinformatics 20(17):3236–3237
Article
Google Scholar
Li MS, Klimov DK, Thirumalai D (2002) Folding in lattice models with side chains. Comput Phys Commun 147(1):625–628
Article
Google Scholar
Lobo FG, Lima CF, Michalewicz Z (2007) Parameter setting in evolutionary algorithms. Springer, New York
Book
Google Scholar
Lopes HS (2008) Evolutionary algorithms for the protein folding problem: a review and current trends. In: Computational intelligence in biomedicine and bioinformatics, vol I. Springer, Heidelberg, pp 297–315
Chapter
Google Scholar
Lopes HS, Scapin MP (2005) An enhanced genetic algorithm for protein structure prediction using the 2D hydrophobic-polar model. Lect Notes Comput Sci 3871:238–246
Article
Google Scholar
Maruo MH, Lopes HS, Delgado MRB (2005) Self-adapting evolutionary parameters: encoding aspects for combinatorial optimization problems. Lect Notes Comput Sci 3448:154–165
Article
Google Scholar
Matsumoto M, Nishimura T (1998) Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator. ACM Trans Model Comput Simul 8(1):3–30
Article
Google Scholar
Nelson DL, Cox MM (2008) Lehninger principles of biochemistry, 5th edn. Freeman, New York
Google Scholar
Scapin MP, Lopes HS (2007) A hybrid genetic algorithm for the protein folding problem using the 2D-HP lattice model. In: Yang A, Shan Y, Bui LT (eds) Success in evolutionary computation. Studies in computational intelligence, vol 92. Springer, Heidelberg, pp 205–224
Google Scholar
Song J, Cheng J, Zheng T, Mao J (2005) A novel genetic algorithm for hp model protein folding. In: Proceedings of 6th international conference on parallel and distributed computing applications and technologies. IEEE Computer Society, Washington, pp 935–937
Google Scholar
Unger R, Moult J (1993) A genetic algorithm for 3D protein folding simulations. In: Proceedings of the 5th annual international conference on genetic algorithms, pp 581–588
Yue K, Dill KA (1993) Sequence-structure relationships in proteins and copolymers. Phys Rev E 48(3):2267–2278
Google Scholar