Score_set: a CAPRI benchmark for scoring ...
Document type :
Article dans une revue scientifique
DOI :
PMID :
Permalink :
Title :
Score_set: a CAPRI benchmark for scoring protein complexes
Author(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]

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]
Journal title :
Proteins
Abbreviated title :
Proteins
Volume number :
82
Pages :
3163-3169
Publication date :
2014-11
ISSN :
1097-0134
English keyword(s) :
Protein-protein docking
Capri
Databases, Protein
scoring function
Models, Molecular
Molecular Docking Simulation
Internet
Protein–protein interaction
Protein Interaction Mapping
benchmark set
computational docking
Capri
Databases, Protein
scoring function
Models, Molecular
Molecular Docking Simulation
Internet
Protein–protein interaction
Protein Interaction Mapping
benchmark set
computational docking
HAL domain(s) :
Chimie/Chimie théorique et/ou physique
English abstract : [en]
Critical Assessment of PRedicted Interactions (CAPRI) has proven to be a catalyst for the development of docking algorithms. An essential step in docking is the scoring of predicted binding modes in order to identify stable ...
Show more >Critical Assessment of PRedicted Interactions (CAPRI) has proven to be a catalyst for the development of docking algorithms. An essential step in docking is the scoring of predicted binding modes in order to identify stable complexes. In 2005, CAPRI introduced the scoring experiment, where upon completion of a prediction round, a larger set of models predicted by different groups and comprising both correct and incorrect binding modes, is made available to all participants for testing new scoring functions independently from docking calculations. Here we present an expanded benchmark data set for testing scoring functions, which comprises the consolidated ensemble of predicted complexes made available in the CAPRI scoring experiment since its inception. This consolidated scoring benchmark contains predicted complexes for 15 published CAPRI targets. These targets were subjected to 23 CAPRI assessments, due to existence of multiple binding modes for some targets. The benchmark contains more than 19,000 protein complexes. About 10% of the complexes represent docking predictions of acceptable quality or better, the remainder represent incorrect solutions (decoys). The benchmark set contains models predicted by 47 different predictor groups including web servers, which use different docking and scoring procedures, and is arguably as diverse as one may expect, representing the state of the art in protein docking. The data set is publicly available at the following URL: http://cb.iri.univ-lille1.fr/Users/lensink/Score_set.Show less >
Show more >Critical Assessment of PRedicted Interactions (CAPRI) has proven to be a catalyst for the development of docking algorithms. An essential step in docking is the scoring of predicted binding modes in order to identify stable complexes. In 2005, CAPRI introduced the scoring experiment, where upon completion of a prediction round, a larger set of models predicted by different groups and comprising both correct and incorrect binding modes, is made available to all participants for testing new scoring functions independently from docking calculations. Here we present an expanded benchmark data set for testing scoring functions, which comprises the consolidated ensemble of predicted complexes made available in the CAPRI scoring experiment since its inception. This consolidated scoring benchmark contains predicted complexes for 15 published CAPRI targets. These targets were subjected to 23 CAPRI assessments, due to existence of multiple binding modes for some targets. The benchmark contains more than 19,000 protein complexes. About 10% of the complexes represent docking predictions of acceptable quality or better, the remainder represent incorrect solutions (decoys). The benchmark set contains models predicted by 47 different predictor groups including web servers, which use different docking and scoring procedures, and is arguably as diverse as one may expect, representing the state of the art in protein docking. The data set is publicly available at the following URL: http://cb.iri.univ-lille1.fr/Users/lensink/Score_set.Show less >
Language :
Anglais
Audience :
Non spécifiée
Administrative institution(s) :
CNRS
Université de Lille
Université de Lille
Research team(s) :
Computational Molecular Systems Biology
Submission date :
2020-02-12T15:11:15Z
2021-03-18T08:21:14Z
2021-03-18T08:21:14Z