Recent Advances in Protein−Ligand Interactions: Molecular Dynamics Simulations and Binding Free Energy
Kshatresh Dutta Dubey,
Rakesh Kumar Tiwari,
Rajendra Prasad Ojha.
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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