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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
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OPTIMIZATION OF SCORING FUNCTION DOCKING FOR ANTIVIRAL DRUG DESIGN AGAINST CORONAVIRUS GENUS Rev Salud Anim.
Pérez,L.J; Díaz de Arce,Heidy.
The development of a wide-spectrum antiviral drug against pathogenic coronavirus is nowadays a attractive prospect and may provide an effective first line of defense against emerging CoV-related diseases. The most attractive target for the design of anticoronaviral inhibitors is the main protease or 3CL PRO. Ligand docking and screening algorithms are now frequently used in the drug-design process. The aim of this work based on a validation study of scoring functions is to find a consensus function or to select the scoring function that better predicts the orientation of the ligand in the pocket binding site, in order to perform a virtual screening in ligand databases, with a lower computational cost in the intent of finding a leader compound for antiviral...
Tipo: Journal article Palavras-chave: Docking algorithms; Scoring functions; Rigid docking; Flexible docking; Main protease.
Ano: 2008 URL: http://scielo.sld.cu/scielo.php?script=sci_arttext&pid=S0253-570X2008000300003
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