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

Marc Lensink; Guillaume Brysbaert; Théo Mauri; Nurul Nadzirin; Sameer Velankar; Raphael Chaleil; Tereza Clarence; Paul Bates; Ren Kong; Bin Liu; Guangbo Yang; Ming Liu; Hang Shi; Xufeng Lu; Shan Chang; Raj Roy; Farhan Quadir; Jian Liu; Jianlin Cheng; Anna Antoniak; Cezary Czaplewski; Artur Giełdoń; Mateusz Kogut; Agnieszka Lipska; Adam Liwo; Emilia Lubecka; Martyna Maszota-zieleniak; Adam Sieradzan; Rafał Ślusarz; Patryk Wesołowski; Karolina Zięba; Carlos del Carpio Muñoz; Eiichiro Ichiishi; Ameya Harmalkar; Jeffrey Gray; Alexandre Bonvin; Francesco Ambrosetti; Rodrigo Vargas Honorato; Zuzana Jandova; Brian Jiménez-garcía; Panagiotis Koukos; Siri van Keulen; Charlotte van Noort; Manon Réau; Jorge Roel-touris; Sergei Kotelnikov; Dzmitry Padhorny; Kathryn Porter; Andrey Alekseenko; Mikhail Ignatov; Israel Desta; Ryota Ashizawa; Zhuyezi Sun; Usman Ghani; Nasser Hashemi; Sandor Vajda; Dima Kozakov; Mireia Rosell; Luis Rodríguez-lumbreras; Juan Fernandez-recio; Agnieszka Karczynska; Sergei Grudinin; Yumeng Yan; Hao Li; Peicong Lin; Sheng‐you Huang; Charles Christoffer; Genki Terashi; Jacob Verburgt; Daipayan Sarkar; Tunde Aderinwale; Xiao Wang; Daisuke Kihara; Tsukasa Nakamura; Yuya Hanazono; Ragul Gowthaman; Johnathan Guest; Rui Yin; Ghazaleh Taherzadeh; Brian Pierce; Didier Barradas-bautista; Zhen Cao; Luigi Cavallo; Romina Oliva; Yuanfei Sun; Shaowen Zhu; Yang Shen; Taeyong Park; Hyeonuk Woo; Jinsol Yang; Sohee Kwon; Jonghun Won; Chaok Seok; Yasuomi Kiyota; Shinpei Kobayashi; Yoshiki Harada; Mayuko Takeda-shitaka; Petras Kundrotas; Amar Singh; Ilya Vakser; Donald Danforth Plant Science Center, St. Louis, MO (United States)

doi:10.1002/prot.26222

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

Journal article

Peer reviewed

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

Marc Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael Chaleil, Tereza Clarence, Paul Bates, Ren Kong, Bin Liu, …

Proteins, structure, function, and bioinformatics, Vol.89(12), pp.1800-1823

12/2021

DOI: https://doi.org/10.1002/prot.26222

PMCID: 8616814

PMID: 34453465

Abstract

Life Sciences

We present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 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 8 automatic servers submitted ~1250 models per target. Twenty groups including 6 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 5 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.

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Title: Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
Creators - without role: Marc Lensink - Unité de Glycobiologie Structurale et Fonctionnelle
Guillaume Brysbaert - Unité de Glycobiologie Structurale et Fonctionnelle
Théo Mauri - Unité de Glycobiologie Structurale et Fonctionnelle
Nurul Nadzirin - European Bioinformatics Institute
Sameer Velankar - European Bioinformatics Institute
Raphael Chaleil - Biomolecular Modelling Laboratory [London]
Tereza Clarence - The Francis Crick Institute
Paul Bates - The Francis Crick Institute
Ren Kong - Jiangsu University of Technology
Bin Liu - Jiangsu University of Technology
Guangbo Yang - Jiangsu University of Technology
Ming Liu - Jiangsu University of Technology
Hang Shi - Jiangsu University of Technology
Xufeng Lu - Jiangsu University of Technology
Shan Chang - Jiangsu University of Technology
Raj Roy - University of Missouri
Farhan Quadir - University of Missouri
Jian Liu - University of Missouri
Jianlin Cheng - University of Missouri
Anna Antoniak - University of Gdańsk
Cezary Czaplewski - University of Gdańsk
Artur Giełdoń - University of Gdańsk
Mateusz Kogut - University of Gdańsk
Agnieszka Lipska - University of Gdańsk
Adam Liwo - University of Gdańsk
Emilia Lubecka - Gdańsk University of Technology
Martyna Maszota-zieleniak - University of Gdańsk
Adam Sieradzan - University of Gdańsk
Rafał Ślusarz - University of Gdańsk
Patryk Wesołowski - University of Gdańsk
Karolina Zięba - University of Gdańsk
Carlos del Carpio Muñoz - Nagoya City University
Eiichiro Ichiishi - International University of Health and Welfare
Ameya Harmalkar - Johns Hopkins University
Jeffrey Gray - Johns Hopkins University
Alexandre Bonvin - Utrecht University
Francesco Ambrosetti - Utrecht University
Rodrigo Vargas Honorato - Bijvoet Center of Biomolecular Research [Utrecht]
Zuzana Jandova - Utrecht University
Brian Jiménez-garcía - Utrecht University
Panagiotis Koukos - Utrecht University
Siri van Keulen - Utrecht University
Charlotte van Noort - Utrecht University
Manon Réau - Utrecht University
Jorge Roel-touris - Utrecht University
Sergei Kotelnikov - Stony Brook University
Dzmitry Padhorny - Stony Brook University
Kathryn Porter - Boston University
Andrey Alekseenko - Stony Brook University
Mikhail Ignatov - Stony Brook University
Israel Desta - Boston University
Ryota Ashizawa - Stony Brook University
Zhuyezi Sun - Boston University
Usman Ghani - Boston University
Nasser Hashemi - Boston University
Sandor Vajda - Boston University
Dima Kozakov - Stony Brook University
Mireia Rosell - Barcelona Supercomputing Center
Luis Rodríguez-lumbreras - Barcelona Supercomputing Center
Juan Fernandez-recio - Gobierno de La Rioja
Agnieszka Karczynska - Université Grenoble Alpes
Sergei Grudinin - Université Grenoble Alpes
Yumeng Yan - Huazhong University of Science and Technology
Hao Li - Huazhong University of Science and Technology
Peicong Lin - Huazhong University of Science and Technology
Sheng‐you Huang - Huazhong University of Science and Technology
Charles Christoffer - Purdue University West Lafayette
Genki Terashi - Purdue University West Lafayette
Jacob Verburgt - Purdue University West Lafayette
Daipayan Sarkar - Purdue University West Lafayette
Tunde Aderinwale - Purdue University West Lafayette
Xiao Wang - Purdue University West Lafayette
Daisuke Kihara - Purdue University West Lafayette
Tsukasa Nakamura - Tohoku University
Yuya Hanazono - National Institutes for Quantum and Radiological Science and Technology
Ragul Gowthaman - Advanced Bioscience Laboratories
Johnathan Guest - Advanced Bioscience Laboratories
Rui Yin - Advanced Bioscience Laboratories
Ghazaleh Taherzadeh - Advanced Bioscience Laboratories
Brian Pierce - Advanced Bioscience Laboratories
Didier Barradas-bautista - King Abdullah University of Science and Technology
Zhen Cao - King Abdullah University of Science and Technology
Luigi Cavallo - King Abdullah University of Science and Technology
Romina Oliva - Parthenope University of Naples
Yuanfei Sun - Texas A&M University
Shaowen Zhu - Texas A&M University
Yang Shen - Texas A&M University
Taeyong Park - Seoul National University
Hyeonuk Woo - Seoul National University
Jinsol Yang - Seoul National University
Sohee Kwon - Seoul National University
Jonghun Won - Seoul National University
Chaok Seok - Seoul National University
Yasuomi Kiyota - Kitasato University
Shinpei Kobayashi - Kitasato University
Yoshiki Harada - Kitasato University
Mayuko Takeda-shitaka - Kitasato University
Petras Kundrotas - University of Kansas
Amar Singh - University of Kansas
Ilya Vakser - University of Kansas
Donald Danforth Plant Science Center, St. Louis, MO (United States)
Publication Details: Proteins, structure, function, and bioinformatics, Vol.89(12), pp.1800-1823
Publisher: Wiley
Identifiers: 9943901408331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article