Molecular Recognition: Computational Analysis and Modelling

Abstract Molecular recognition is critical to many fundamental processes in biology, including enzymatic reactions, signal transduction, genetic information processing, as well as molecular and cellular transport. The question of how proteins selectively recognize and correctly associate with their partners is an active research problem. For many proteins, experimental information about the structures of their molecular complexes and the details of their interactions are lacking. Macromolecular, structure-based computational techniques provide a means to predict the interactions of proteins and to investigate their recognition mechanisms. Here, we first discuss the general mechanism of molecular recognition as a multistep process from diffusion of one molecule toward the second to tight complex formation. We then describe the main forces and the physical properties that govern biomolecular interactions and introduce the principles of modeling them. Finally, simulation methods and computational approaches for molecular docking are briefly presented.