Protein-Protein Docking Dealing With the Unknown

Abstract

Protein-protein binding is one of the critical events in biology, and knowledge of proteic complexesthree-dimensional structures is of fundamental importance for the biochemical study of pharmacologic compounds.In the past two decades there was an emergence of a large variety of algorithms designed to predict the structures ofprotein-protein complexes-a procedure named docking. Computational methods, if accurate and reliable, couldplay an important role, both to infer functional properties and to guide new experiments. Despite the outstandingprogress of the methodologies developed in this area, a few problems still prevent protein-protein docking to be awidespread practice in the structural study of proteins. In this review we focus our attention on the principles thatgovern docking, namely the algorithms used for searching and scoring, which are usually referred as the dockingproblem. We also focus our attention on the use of a flexible description of the proteins under study and the use ofbiological information as the localization of the hot spots, the important residues for protein-protein binding. Themost common docking softwares are described too.