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 proteinligand 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 structurebased virtual screening, molecular dynamics simulations play a pivotal role in understanding the features that are important for ligandbinding 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.
Keywords: Molecular dynamics, computer simulations, enoyl-[acyl-carrier-protein] reductase (InhA), purine nucleoside phosphorylase (PNP), shikimate kinase, Mycobacterium tuberculosis, GROMACS, structure-based virtual screening, Protein Targets, hydrogen bonds
Current Medicinal Chemistry
Title: Molecular Dynamics Simulations of Protein Targets Identified in Mycobacterium tuberculosis
Volume: 18 Issue: 9
Author(s): W. F. de Azevedo
Affiliation:
Keywords: Molecular dynamics, computer simulations, enoyl-[acyl-carrier-protein] reductase (InhA), purine nucleoside phosphorylase (PNP), shikimate kinase, Mycobacterium tuberculosis, GROMACS, structure-based virtual screening, Protein Targets, hydrogen bonds
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 proteinligand 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 structurebased virtual screening, molecular dynamics simulations play a pivotal role in understanding the features that are important for ligandbinding 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.
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Cite this article as:
F. de Azevedo W., Molecular Dynamics Simulations of Protein Targets Identified in Mycobacterium tuberculosis, Current Medicinal Chemistry 2011; 18 (9) . https://dx.doi.org/10.2174/092986711795029519
DOI https://dx.doi.org/10.2174/092986711795029519 |
Print ISSN 0929-8673 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-533X |
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