Protein docking using case-based reasoning.
Fiche publication
Date publication
décembre 2013
Auteurs
Membres identifiés du Cancéropôle Est :
Dr DEVIGNES Marie-Dominique
Tous les auteurs :
Ghoorah AW, Devignes MD, Smail-Tabbone M, Ritchie DW
Lien Pubmed
Résumé
Protein docking algorithms aim to calculate the three-dimensional (3D) structure of a protein complex starting from its unbound components. Although ab initio docking algorithms are improving, there is a growing need to use homology modeling techniques to exploit the rapidly increasing volumes of structural information that now exist. However, most current homology modeling approaches involve finding a pair of complete single-chain structures in a homologous protein complex to use as a 3D template, despite the fact that protein complexes are often formed from one or more domain-domain interactions (DDIs). To model 3D protein complexes by domain-domain homology, we have developed a case-based reasoning approach called KBDOCK which systematically identifies and reuses domain family binding sites from our database of nonredundant DDIs. When tested on 54 protein complexes from the Protein Docking Benchmark, our approach provides a near-perfect way to model single-domain protein complexes when full-homology templates are available, and it extends our ability to model more difficult cases when only partial or incomplete templates exist. These promising early results highlight the need for a new and diverse docking benchmark set, specifically designed to assess homology docking approaches.
Référence
Proteins. 2013 Dec;81(12):2150-8