Binding affinity of protein-protein complexes: Experimental techniques, databases and computational methods

Protein-protein interactions (PPIs) are important for several cellular processes. The principles governing the recognition of protein-protein complexes are investigated using the information on binding-site residues at the interface, specific non-covalent interactions as well as binding affinity. Experimentally, binding affinity of PPIs is studied with isothermal titration calorimetry, surface plasmon resonance and fluorescence- based techniques. On the other hand, computational methods have been developed to understand/predict the binding affinity and the effects of mutations. In this chapter, with a brief introduction on the concept of binding affinity, we outline the experimental techniques to explore the binding affinity of protein-protein complexes along with computational analysis and prediction of binding affinity. Further, we illustrate the utilities and applications of PROXiMATE database for binding affinity of protein-protein complexes and their mutants as well as effects of mutations on binding affinity.