Development of a method / software (PL-DOCK) for Protein-Ligand Docking Using Genetic Algorithms and Rotamer library. Systems Targets: HIV protease-1 and dihydrofolate reductase / Desenvolvimento de um método/software (PL-DOCK) para o Docking Proteína-Ligante usando algoritmos genéticos e Biblioteca de Rotâmeros. Sistemas Alvos: protease do HIV-1 e Diidrofolato Redutase

AUTOR(ES)
FONTE

IBICT - Instituto Brasileiro de Informação em Ciência e Tecnologia

DATA DE PUBLICAÇÃO

19/07/2010

RESUMO

We describe a new software, PL-DOCK (Protein-Ligand Dock), that combines genetic algorithm and rotamer library in order to achieve protein-ligand rigid and semi-flexible docking simulations. This program compose a methodology/software bigger that take combines GA, rotamer library and normal modes analysis to simulate protein-ligand and protein-protein docking into account local conformational adjustments as well as the induced fit mechanism implying the whole structure. The PL-DOCK uses a rotamer library for changing the side chains conformations within and around the binding site. The Force-Field PL-DOCK has unbound and a implicit solvation term. We describe only the methodology and discuss the results and the performance obtained. The PL-DOCK was applied to study two complexes: HIV-1 ASPARTYL PROTEASE and DMP323 as ligand and Dihydrofolate reductase (DHFR) and MTX as ligand.

ASSUNTO(S)

docking pl-dock - software docking pl-dock - software simulação - software biofisica molecular simulation - software

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