Titre :

Docking, scoring, and affinity prediction in CAPRI

Auteur(s) :

Lensink, Marc [Auteur]
Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 [UGSF]
Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] [IRI]
Wodak, Shoshana J. [Auteur]
University of Toronto
The Hospital for sick children [Toronto] [SickKids]

Titre de la revue :

Proteins

Nom court de la revue :

Proteins

Numéro :

81

Pagination :

2082-2095

Date de publication :

2013-12

ISSN :

1097-0134

Mot(s)-clé(s) en anglais :

Water
Humans
Computational Biology
interface water molecules
Protein interactions
Protein Interaction Mapping
Proteins
Capri
Blind prediction
Protein Binding
Docking
Ligands
Protein Conformation
Molecular Docking Simulation
Software
affinity

Discipline(s) HAL :

Chimie/Chimie théorique et/ou physique

Résumé en anglais : [en]

We present the fifth evaluation of docking and related scoring methods used in the community-wide experiment on the Critical Assessment of Predicted Interactions (CAPRI). The evaluation examined predictions submitted for ...
Lire la suite >We present the fifth evaluation of docking and related scoring methods used in the community-wide experiment on the Critical Assessment of Predicted Interactions (CAPRI). The evaluation examined predictions submitted for a total of 15 targets in eight CAPRI rounds held during the years 2010-2012. The targets represented one the most diverse set tackled by the CAPRI community so far. They included only 10 "classical" docking and scoring problems. In one of the classical targets, the new challenge was to predict the position of water molecules in the protein-protein interface. The remaining five targets represented other new challenges that involved estimating the relative binding affinity and the effect of point mutations on the stability of designed and natural protein-protein complexes. Although the 10 classical CAPRI targets included two difficult multicomponent systems, and a protein-oligosaccharide complex with which CAPRI participants had little experience, this evaluation indicates that the performance of docking and scoring methods has remained quite robust. More remarkably, we find that automatic docking servers exhibit a significantly improved performance, with some servers now performing on par with predictions done by humans. The performance of CAPRI participants in the new challenges, briefly reviewed here, was mediocre overall, but some groups did relatively well and their approaches suggested ways of improving methods for designing binders and for estimating the free energies of protein assemblies, which should impact the field of protein modeling and design as a whole.Lire moins >

Langue :

Anglais

Audience :

Non spécifiée

Établissement(s) :

CNRS
Université de Lille

Collections :

• Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576

Équipe(s) de recherche :

Computational Molecular Systems Biology

Date de dépôt :

2020-02-12T15:11:14Z
2021-03-18T08:14:38Z