Protein-Protein Docking Dealing With the Unknown

• Type: Another Publication in an International Scientific Journal
• Date: 2010

Authors

Irina S Moreira (Author) Other; Pedro A Fernandes (Author) FCUP; Maria J Ramos (Author) FCUP

Journal

Title: Journal of Computational Chemistry

Vol. 31 No. 2

Pages: 317-342

ISSN: 0192-8651

Publisher: Wiley-Blackwell

Indexing

ISI Web of Knowledge - 89 Citations

Scopus - 94 Citations

Scientific classification

FOS: Natural sciences > Chemical sciences

Other information

Authenticus ID: P-003-9NH

DOI: 10.1002/jcc.21276

Abstract (EN): 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 clocking. 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 clocking to be a widespread practice in the structural study of proteins. In this review we focus our attention on the principles that govern clocking, 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 clocking softwares are described too. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 31: 317-342, 2010

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 26