Data/hora: 03/06/2024 03:35:36

Provedor de dados: | 74
País: | Brazil
Título: | A genetic algorithm for the ligand-protein docking problem
Autores: | Magalhães,Camila S. de; Barbosa,Hélio J.C.; Dardenne,Laurent E.
Data: | 2004-01-01
Ano: | 2004
Palavras-chave: | Ligand-protein docking; Flexible docking; Genetic algorithms.
Resumo: | 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 rigid docking, and 0.420 Å to 1.943 Å in the flexible docking. We found that not only the number of ligand conformational degrees of freedom is an important aspect to the algorithm performance, but also that the more internal dihedral angles are critical. Furthermore, our results showed that the initial population distribution can be relevant for the algorithm performance.
Tipo: | Info:eu-repo/semantics/article
Idioma: | Inglês
Identificador: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400022
Editor: | Sociedade Brasileira de Genética
Relação: | 10.1590/S1415-47572004000400022
Formato: | text/html
Fonte: | Genetics and Molecular Biology  v.27 n.4 2004
Fonte: | info:eu-repo/semantics/openAccess