Recent advances in protein-ligand interactions: molecular dynamics simulations and binding free energy

Computational techniques are one of the most emerging topics in structural and molecular biology. Molecular dynamics (MD) simulations are used not only to explore the conformational aspects of biological systems but also to have significant scope in protein-ligand interactions. Then the binding free...

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Published inCurrent computer-aided drug design Vol. 9; no. 4; p. 518
Main Authors Dubey, Kshatresh Dutta, Tiwari, Rakesh Kumar, Ojha, Rajendra Prasad
Format Journal Article
LanguageEnglish
Published United Arab Emirates 01.12.2013
Subjects
Computational Biology
Humans
Ligands
Molecular Conformation
Molecular Dynamics Simulation
Protein Binding
Proteins - chemistry
Proteins - metabolism
Thermodynamics
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Summary:Computational techniques are one of the most emerging topics in structural and molecular biology. Molecular dynamics (MD) simulations are used not only to explore the conformational aspects of biological systems but also to have significant scope in protein-ligand interactions. Then the binding free energy calculations are readily applied to the simulated systems in order to predict the binding affinities. The thermodynamic properties are directly related to protein-ligand interactions which are dependent upon a few specific parameters. In the present review, we highlight some facts related to protein-ligand complexes, by starting with a survey of MD simulations and binding free energy calculations and ending with some successful implementations of these computational techniques.
ISSN:1875-6697
DOI:10.2174/15734099113096660036