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	Provedor de dados Genet. Mol. Biol. (3) Autor Dardenne,Laurent E. (3) Barbosa,Hélio J. C. (1) Barbosa,Hélio J.C. (1) Custódio,Fábio L. (1) Dall'Igna Júnior,Alcino (1) Magalhães,Camila S. de (1) Mundim,Kleber C. (1) Silva,Renato S. (1) Mais... Palavra-chave Genetic algorithms (2) Flexible docking (1) Generalized simulated annealing (1) HP model (1) Ligand-protein docking (1) Optimization (1) Protein folding (1) Mais... Tipo do documento Info:eu-repo/semantics/article (3) Ano 2004 (3) País Brazil (3) Idioma Inglês (3)		Ordenar por:  Relevância Autor Título Ano Registros recuperados: 3 Primeira ... 1 ... Última A genetic algorithm for the ligand-protein docking problem Genet. Mol. Biol. Magalhães,Camila S. de; Barbosa,Hélio J.C.; Dardenne,Laurent E.. We analyzed the performance of a real coded "steady-state" genetic algorithm (SSGA) using a grid-based methodology in docking five HIV-1 protease-ligand complexes having known three-dimensional structures. All ligands tested are highly flexible, having more than 10 conformational degrees of freedom. The SSGA was tested for the rigid and flexible ligand docking cases. The implemented genetic algorithm was able to dock successfully rigid and flexible ligand molecules, but with a decreasing performance when the number of ligand conformational degrees of freedom increased. The docked lowest-energy structures have root mean square deviation (RMSD) with respect to the corresponding experimental crystallographic structure ranging from 0.037 Å to 0.090 Å in the... Tipo: Info:eu-repo/semantics/article Palavras-chave: Ligand-protein docking; Flexible docking; Genetic algorithms. Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400022 Investigation of the three-dimensional lattice HP protein folding model using a genetic algorithm Genet. Mol. Biol. Custódio,Fábio L.; Barbosa,Hélio J. C.; Dardenne,Laurent E.. An approach to the hydrophobic-polar (HP) protein folding model was developed using a genetic algorithm (GA) to find the optimal structures on a 3D cubic lattice. A modification was introduced to the scoring system of the original model to improve the model's capacity to generate more natural-like structures. The modification was based on the assumption that it may be preferable for a hydrophobic monomer to have a polar neighbor than to be in direct contact with the polar solvent. The compactness and the segregation criteria were used to compare structures created by the original HP model and by the modified one. An islands' algorithm, a new selection scheme and multiple-points crossover were used to improve the performance of the algorithm. Ten sequences,... Tipo: Info:eu-repo/semantics/article Palavras-chave: HP model; Genetic algorithms; Protein folding. Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400023 Performance and parameterization of the algorithm Simplified Generalized Simulated Annealing Genet. Mol. Biol. Dall'Igna Júnior,Alcino; Silva,Renato S.; Mundim,Kleber C.; Dardenne,Laurent E.. The main goal of this study is to find the most effective set of parameters for the Simplified Generalized Simulated Annealing algorithm, SGSA, when applied to distinct cost function as well as to find a possible correlation between the values of these parameters sets and some topological characteristics of the hypersurface of the respective cost function. The SGSA algorithm is an extended and simplified derivative of the GSA algorithm, a Markovian stochastic process based on Tsallis statistics that has been used in many classes of problems, in particular, in biological molecular systems optimization. In all but one of the studied cost functions, the global minimum was found in 100% of the 50 runs. For these functions the best visiting parameter, qV,... Tipo: Info:eu-repo/semantics/article Palavras-chave: Optimization; Generalized simulated annealing. Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400024 Registros recuperados: 3 Primeira ... 1 ... Última

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