Computational tools have been used extensively to examine protein-protein and protein-ligand interactions. Continuum electrostatics calculations and molecular dynamics simulations can provide insight into the structural stability, binding, and function of proteins, and in turn can serve as predictive tools for guiding the design of experiments to probe specific molecular phenomena. In this review, we describe methods and tools used to understand protein interactions, and discuss steps taken toward improvement and optimization of these methods. We also describe a number of applications of in silico modeling tools to protein interactions with implications in pathogenic infections and autoimmune disorders.
Keywords: Molecular dynamics simulations, Continuum electrostatic calculations, Protein-ligand interactions, Protein-protein interactions, Free energy, Solvation, Ionization, Clustering measures, Immune system proteins, Immune system regulation and inhibition