Physics- and Chemistry-based Computational Approaches to Ligand Binding for Proteins

Abstract

We review theoretical and computational approaches to ligand binding, one of the most relevant biomolecular events in a cell. Starting from a kinetic description of ligand binding, which is summarized by the use of the dissociation constant, we discuss simple docking simulations, the Molecular Mechanics/Poisson-Boltzmann Surface Area (Generalized Born Surface Area) approximation for binding free energy (intermediate level of approximation) , and more rigorous free energy profile calculations, which will be used in the near future for designing and discovering drugs.