The elucidation of the interactions between a protein and a ligand or proteins is a key
issue for understanding of functional processes of various proteins, enzymes and receptors in biological
organisms, system biology and drug design. One of the most important matters in these
problems is the accurate estimation of binding free energy between a protein and a ligand or proteins.
In the present review, we overview various techniques and introduce a new technique for estimation
of binding free energy calculations. We also discuss possible ways to incorporate the effect of
fect of solvent.
Keywords: Binding free energy, Drug design, Biological processes, Free energy variational principle, Molecular dynamics
simulations, Solvent model.
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