Current Computer-Aided Drug Design

Subhash C. Basak
Departments of Chemistry, Biochemistry & Molecular Biology University of Minnesota Duluth
Duluth, MN 55811
USA

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Recent Advances in Protein−Ligand Interactions: Molecular Dynamics Simulations and Binding Free Energy

Author(s): Kshatresh Dutta Dubey, Rakesh Kumar Tiwari, Rajendra Prasad Ojha.

Abstract:

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.

Keywords: FEP, LIE, ligand binding, MD simulations, MM-PBSA, QM/MM, thermodynamical parameter.

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Article Details

VOLUME: 9
ISSUE: 4
Year: 2013
Page: [518 - 531]
Pages: 14
DOI: 10.2174/15734099113096660036
Price: $58