Premium
Protein–protein docking dealing with the unknown
Author(s) -
Moreira Irina S.,
Fernandes Pedro A.,
Ramos Maria J.
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21276
Subject(s) - docking (animal) , protein–ligand docking , macromolecular docking , computational biology , computer science , protein structure , protein–protein interaction , artificial intelligence , machine learning , chemistry , biology , drug discovery , bioinformatics , biochemistry , virtual screening , medicine , nursing
Abstract Protein–protein binding is one of the critical events in biology, and knowledge of proteic complexes three‐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 of protein–protein complexes—a procedure named docking. Computational methods, if accurate and reliable, could play an important role, both to infer functional properties and to guide new experiments. Despite the outstanding progress of the methodologies developed in this area, a few problems still prevent protein–protein docking to be a widespread practice in the structural study of proteins. In this review we focus our attention on the principles that govern docking, namely the algorithms used for searching and scoring, which are usually referred as the docking problem. We also focus our attention on the use of a flexible description of the proteins under study and the use of biological information as the localization of the hot spots, the important residues for protein–protein binding. The most common docking softwares are described too. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010