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Curr Med Chem. 2011;18(9):1353-66.

Molecular dynamics simulations of protein targets identified in Mycobacterium tuberculosis.

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1
Instituto Nacional de Ciência e Tecnologia em Tuberculose-CNPq-MCT, Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre - RS, Brazil. walter@azevedolab.net

Abstract

Application of molecular dynamics simulation technique has become a conventional computational methodology to calculate significant processes at the molecular level. This computational methodology is particularly useful for analyzing the dynamics of protein-ligand systems. Several uses of molecular dynamics simulation makes possible evaluation of important structural features found at interface between a ligand and a protein, such as intermolecular hydrogen bonds, contact area and binding energy. Considering structure-based virtual screening, molecular dynamics simulations play a pivotal role in understanding the features that are important for ligand-binding affinity. This information could be employed to select higher-affinity ligands obtained in screening processes. Many protein targets such as enoyl-[acyl-carrier-protein] reductase (InhA), purine nucleoside phosphorylase (PNP), and shikimate kinase have been submitted to these simulations and will be analyzed here. All command files used in this review are available for download at http://azevedolab.net/md_75.html.

PMID:
21366529
[Indexed for MEDLINE]
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