From Multiple Protein Docking to Protein–Protein Docking at Interactome Level

Molecular docking is used to anticipate the optimal orientation of a particular molecule to a target to form a stable complex. It makes predictions about the 3D structure of any complex based on the binding characteristics of the ligand and the target receptor usually a protein. It is an exceptionally useful tool, which is used as a model to study how ligands attach to proteins. Docking can also be used for studying the interaction of ligands and proteins to analyze inhibitory efficacy. The ligand may also be a protein, making it possible to study interactions between two different proteins using the numerous docking tools available for basic research on protein interactions. The protein–protein docking is a crucial approach to understanding the protein interactions and predicting the structure of protein complexes that have not yet been experimentally determined. Moreover, the protein–protein interactions can predict the function of target proteins and the drug-like properties of molecules. Therefore, protein docking assists in uncovering insights into protein interactions and also aids in a better understanding of molecular pathways/mechanisms. This chapter comprehends the various tools for protein–protein docking (pairwise and multiple), including their methodologies and analysis of output as results.