Title :

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

Author(s) :

Lensink, Marc [Auteur]
Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576
Velankar, Sameer [Auteur]
European Bioinformatics Institute [Hinxton] [EMBL-EBI]
Wodak, Shoshana J. [Auteur]
VIB-VUB Center for Structural Biology [Bruxelles]

Journal title :

Proteins

Abbreviated title :

Proteins

Volume number :

85

Pages :

359-377

Publication date :

2017-03

ISSN :

1097-0134

English keyword(s) :

Water
protein docking
Peptides
Humans
Multiprotein Complexes
Computational Biology
Benchmarking
protein-peptide interation
Protein Interaction Mapping
Proteins
Algorithms
Capri
water modeling
Protein Binding
Blind prediction
Protein Conformation
Nucleosomes
Molecular Docking Simulation
Software
Binding Sites
Research Design

HAL domain(s) :

Chimie/Chimie théorique et/ou physique

English abstract : [en]

We present the sixth report evaluating the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of ...
Show more >We present the sixth report evaluating the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions (CAPRI). The evaluation is based on a total of 20,670 predicted models for 8 protein-peptide complexes, a novel category of targets in CAPRI, and 12 protein-protein targets in CAPRI prediction Rounds held during the years 2013-2016. For two of the protein-protein targets, the focus was on the prediction of side-chain conformation and positions of interfacial water molecules. Seven of the protein-protein targets were particularly challenging owing to their multicomponent nature, to conformational changes at the binding site, or to a combination of both. Encouragingly, the very large multiprotein complex with the nucleosome was correctly predicted, and correct models were submitted for the protein-peptide targets, but not for some of the challenging protein-protein targets. Models of acceptable quality or better were obtained for 14 of the 20 targets, including medium quality models for 13 targets and high quality models for 8 targets, indicating tangible progress of present-day computational methods in modeling protein complexes with increased accuracy. Our evaluation suggests that the progress stems from better integration of different modeling tools with docking procedures, as well as the use of more sophisticated evolutionary information to score models. Nonetheless, adequate modeling of conformational flexibility in interacting proteins remains an important area with a crucial need for improvement. Proteins 2017; 85:359-377. © 2016 Wiley Periodicals, Inc.Show less >

Language :

Anglais

Audience :

Internationale

Popular science :

Non

Administrative institution(s) :

CNRS
Université de Lille

Collections :

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

Research team(s) :

Computational Molecular Systems Biology

Submission date :

2020-02-12T15:11:20Z
2021-07-15T06:38:15Z