title: Recent advances in protein-ligand interactions: molecular dynamics simulations and binding free energy.
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.
authors.forename: Kshatresh Dutta
authors.initials: KD
authors.lastname: Dubey
authors.forename: Rakesh Kumar
authors.initials: RK
authors.lastname: Tiwari
authors.affiliation: Biophysics Unit, Department of Physics, DDU Gorakhpur University, India. rp_ojha@yahoo.com.
authors.forename: Rajendra Prasad
authors.initials: RP
authors.lastname: Ojha
mesh_terms: D019295:Computational Biology; D006801:Humans; D008024:Ligands; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D008024:Ligands; D011506:Proteins