The structural analysis of protein-protein interactions and the prediction of their functional properties are important areas in modern structural bioinformatics. First, we review concepts for classifying protein-protein interactions, and for analyzing the geometry and composition of binding interfaces. Next, computational methods are discussed that allow predicting hot-spot residues and the kinetics and the rmodynamics of binding. Then, we focus on the mode of action of small molecule effectors that may either act as competitive antagonists of protein binders or as allosteric modulators. Here, we emphasize the roles of pre-formed or transiently open ligand-binding pockets at protein-protein interfaces. The presentation is rounded up by an overview over databases on protein-protein and protein-small-molecule interactions.
Keywords: Allosteric modulator, binding interface, competitive antagonist, hot-spot residue, obligate interaction, protein complex classification, protein-protein database, PDK1, transient binding pocket, molecule