Desenvolvimento de uma abordagem para docking proteína ligante por meio de algoritmos genéticos e modos normais / Development of an approach to ligand docking protein through genetic algorithms and normal modes

AUTOR(ES)
FONTE

IBICT - Instituto Brasileiro de Informação em Ciência e Tecnologia

DATA DE PUBLICAÇÃO

21/09/2010

RESUMO

The molecular recognition process is important to the life and it is present in different cellular mechanisms. The activity of several molecular processes depends on molecules (ligands) that recognize specific bonding sites (receptors) and binds to them. The processes of molecular recognition are very important for the drug development. Molecular Docking is an important technique for the drug design process. One great challenge for these techniques is implementation of complete flexibility of the receptor molecule and a solvent explicit model. In this work, we propose and implement part of a methodology (called GANM) that considers the flexibility of side chains of receptor, effects of solvent and the flexibility of backbone. The methodology GANM uses Genetic Algorithms, Rotamers Library (for the flexibility of side chain), normal modes analysis and implicit solvatation to simulate the docking protein-ligand. The software developed (PL-DOCK) for the first version of GANM was tested through cross-docking experiments with the following complexes: HIV-1 protease/Nelfinavir, HIV-1 protease/Ritonavir and HIV-1 protease/Indinavir. The first version presents interesting results, most of the simulations showed good values for the RMSD. This work also discusses the implementation and test of a program (NoMPro) to calculate the normal modes of low frequency for proteins

ASSUNTO(S)

outros docking molecular metodologia ganm algoritmos genéticos molecular docking methodology ganm genetic algorithms

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