Title :

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Author(s) :

Lensink, Marc [Auteur]
Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576
Brysbaert, Guillaume [Auteur]
Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576
Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576
Mauri, Theo [Auteur]
Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576
Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576
Nadzirin, Nurul [Auteur]
European Bioinformatics Institute [Hinxton] [EMBL-EBI]
Velankar, Sameer [Auteur]
European Bioinformatics Institute [Hinxton] [EMBL-EBI]
Chaleil, Raphael A. G. [Auteur]
The Francis Crick Institute [London]
Clarence, Tereza [Auteur]
The Francis Crick Institute [London]
Bates, Paul A. [Auteur]
The Francis Crick Institute [London]
Kong, Ren [Auteur]
Jiangsu University of Technology [Changzhou]
Liu, Bin [Auteur]
Jiangsu University of Technology [Changzhou]
Yang, Guangbo [Auteur]
Jiangsu University of Technology [Changzhou]
Liu, Ming [Auteur]
Jiangsu University of Technology [Changzhou]
Shi, Hang [Auteur]
Jiangsu University of Technology [Changzhou]
Lu, Xufeng [Auteur]
Jiangsu University of Technology [Changzhou]
Chang, Shan [Auteur]
Jiangsu University of Technology [Changzhou]
Roy, Raj S. [Auteur]
Department of Electrical Engineering and Computer Science [Columbia] [EECS]
Quadir, Farhan [Auteur]
Department of Electrical Engineering and Computer Science [Columbia] [EECS]
Liu, Jian [Auteur]
Department of Electrical Engineering and Computer Science [Columbia] [EECS]
Cheng, Jianlin [Auteur]
Department of Electrical Engineering and Computer Science [Columbia] [EECS]
Antoniak, Anna [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Czaplewski, Cezary [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Giełdoń, Artur [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Kogut, Mateusz [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Lipska, Agnieszka G. [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Liwo, Adam [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Lubecka, Emilia A. [Auteur]
Faculty of Electronics, Telecommunications and Informatics [GUT Gdańsk] [ETI]
Maszota‐Zieleniak, Martyna [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Sieradzan, Adam K. [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Ślusarz, Rafał [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Wesołowski, Patryk A. [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Zięba, Karolina [Auteur]
Faculty of Chemistry [Univ Gdańsk]
Del Carpio Muñoz, Carlos A. [Auteur]
Graduate School of Medical Sciences [Nagoya]
Ichiishi, Eiichiro [Auteur]
International University of Health and Welfare Hospital [IUHW Hospital]
Harmalkar, Ameya [Auteur]
Johns Hopkins University [JHU]
Gray, Jeffrey J. [Auteur]
Johns Hopkins University [JHU]
Bonvin, Alexandre M. J. J. [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Ambrosetti, Francesco [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Vargas Honorato, Rodrigo [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Jandova, Zuzana [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Jiménez‐García, Brian [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Koukos, Panagiotis I. [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Van Keulen, Siri [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Van Noort, Charlotte W. [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Réau, Manon [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Roel‐Touris, Jorge [Auteur]
Bijvoet Center of Biomolecular Research [Utrecht]
Kotelnikov, Sergei [Auteur]
Stony Brook University [SUNY] [SBU]
Padhorny, Dzmitry [Auteur]
Stony Brook University [SUNY] [SBU]
Porter, Kathryn A. [Auteur]
Department of Biomedical Engineering [Boston]
Alekseenko, Andrey [Auteur]
Stony Brook University [SUNY] [SBU]
Ignatov, Mikhail [Auteur]
Stony Brook University [SUNY] [SBU]
Desta, Israel [Auteur]
Department of Biomedical Engineering [Boston]
Ashizawa, Ryota [Auteur]
Stony Brook University [SUNY] [SBU]
Sun, Zhuyezi [Auteur]
Department of Biomedical Engineering [Boston]
Ghani, Usman [Auteur]
Department of Biomedical Engineering [Boston]
Hashemi, Nasser [Auteur]
Department of Biomedical Engineering [Boston]
Vajda, Sandor [Auteur]
Department of Biomedical Engineering [Boston]
Kozakov, Dima [Auteur]
Stony Brook University [SUNY] [SBU]
Rosell, Mireia [Auteur]
Instituto de Ciencias de la Vid y el Vino [ICVV]
Rodríguez‐Lumbreras, Luis A. [Auteur]
Instituto de Ciencias de la Vid y el Vino [ICVV]
Fernandez‐Recio, Juan [Auteur]
Instituto de Ciencias de la Vid y el Vino [ICVV]
Karczynska, Agnieszka [Auteur]
Inria Grenoble - Rhône-Alpes
Grudinin, Sergei [Auteur]
Inria Grenoble - Rhône-Alpes
Yan, Yumeng [Auteur]
Huazhong University of Science and Technology [Wuhan] [HUST]
Li, Hao [Auteur]
Huazhong University of Science and Technology [Wuhan] [HUST]
Lin, Peicong [Auteur]
Huazhong University of Science and Technology [Wuhan] [HUST]
Huang, Sheng‐You [Auteur]
Huazhong University of Science and Technology [Wuhan] [HUST]
Christoffer, Charles [Auteur]
Indiana University - Purdue University Indianapolis [IUPUI]
Terashi, Genki [Auteur]
Indiana University - Purdue University Indianapolis [IUPUI]
Verburgt, Jacob [Auteur]
Indiana University - Purdue University Indianapolis [IUPUI]
Sarkar, Daipayan [Auteur]
Indiana University - Purdue University Indianapolis [IUPUI]
Aderinwale, Tunde [Auteur]
Indiana University - Purdue University Indianapolis [IUPUI]
Wang, Xiao [Auteur]
Indiana University - Purdue University Indianapolis [IUPUI]
Kihara, Daisuke [Auteur]
Indiana University - Purdue University Indianapolis [IUPUI]
Nakamura, Tsukasa [Auteur]
Graduate School of Information Sciences [Sendaï]
Hanazono, Yuya [Auteur]
National Institutes for Quantum and Radiological Science and Technology [QST]
Gowthaman, Ragul [Auteur]
University of Maryland [Baltimore]
Guest, Johnathan D. [Auteur]
University of Maryland [Baltimore]
Yin, Rui [Auteur]
University of Maryland [Baltimore]
Taherzadeh, Ghazaleh [Auteur]
University of Maryland [Baltimore]
Pierce, Brian G. [Auteur]
University of Maryland [Baltimore]
Barradas‐Bautista, Didier [Auteur]
King Abdullah University of Science and Technology [Saudi Arabia] [KAUST]
Cao, Zhen [Auteur]
King Abdullah University of Science and Technology [Saudi Arabia] [KAUST]
Cavallo, Luigi [Auteur]
King Abdullah University of Science and Technology [Saudi Arabia] [KAUST]
Oliva, Romina [Auteur]
Università degli Studi di Napoli “Parthenope” = University of Naples [PARTHENOPE]
Sun, Yuanfei [Auteur]
Texas A&M University [Galveston]
Zhu, Shaowen [Auteur]
Texas A&M University [Galveston]
Shen, Yang [Auteur]
Texas A&M University [Galveston]
Park, Taeyong [Auteur]
Seoul National University [Seoul] [SNU]
Woo, Hyeonuk [Auteur]
Seoul National University [Seoul] [SNU]
Yang, Jinsol [Auteur]
Seoul National University [Seoul] [SNU]
Kwon, Sohee [Auteur]
Seoul National University [Seoul] [SNU]
Won, Jonghun [Auteur]
Seoul National University [Seoul] [SNU]
Seok, Chaok [Auteur]
Seoul National University [Seoul] [SNU]
Kiyota, Yasuomi [Auteur]
Kitasato University
Kobayashi, Shinpei [Auteur]
Kitasato University
Harada, Yoshiki [Auteur]
Kitasato University
Takeda‐Shitaka, Mayuko [Auteur]
Kitasato University
Kundrotas, Petras J. [Auteur]
University of Kansas [Lawrence] [KU]
Singh, Amar [Auteur]
University of Kansas [Lawrence] [KU]
Vakser, Ilya A. [Auteur]
University of Kansas [Lawrence] [KU]
Dapkūnas, Justas [Auteur]
Vilnius University [Vilnius]
Olechnovič, Kliment [Auteur]
Vilnius University [Vilnius]
Venclovas, Česlovas [Auteur]
Vilnius University [Vilnius]
Duan, Rui [Auteur]
University of Missouri [Columbia] [Mizzou]
Qiu, Liming [Auteur]
University of Missouri [Columbia] [Mizzou]
Xu, Xianjin [Auteur]
University of Missouri [Columbia] [Mizzou]
Zhang, Shuang [Auteur]
University of Missouri [Columbia] [Mizzou]
Zou, Xiaoqin [Auteur]
University of Missouri [Columbia] [Mizzou]
Wodak, Shoshana J. [Auteur]
VIB-VUB Center for Structural Biology [Bruxelles]

Journal title :

Proteins: Structure, Function, and Bioinformatics

Abbreviated title :

Proteins

Volume number :

89

Pages :

1800-1823

Publisher :

Wiley

Publication date :

2021-08-05

ISSN :

0887-3585

English keyword(s) :

blind prediction
CAPRI
CASP
docking
oligomeric state
protein assemblies
protein complexes
protein docking
protein–protein interaction
template-based modeling

HAL domain(s) :

Sciences du Vivant [q-bio]

English abstract : [en]

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order ...
Show more >We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Administrative institution(s) :

Université de Lille
CNRS

Collections :

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

Research team(s) :

Computational Molecular Systems Biology

Submission date :

2022-01-11T10:00:09Z
2022-01-12T10:04:32Z
2022-01-31T10:03:32Z