Prediction of protein assemblies, the next frontier: The <scp>CASP14‐CAPRI</scp> experiment
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- Marc F. Lensink
- CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology University of Lille Lille France
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- Guillaume Brysbaert
- CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology University of Lille Lille France
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- Théo Mauri
- CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology University of Lille Lille France
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- Nurul Nadzirin
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory European Bioinformatics Institute (EMBL‐EBI) Cambridge UK
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- Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory European Bioinformatics Institute (EMBL‐EBI) Cambridge UK
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- Raphael A. G. Chaleil
- Biomolecular Modelling Laboratory The Francis Crick Institute London UK
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- Tereza Clarence
- Biomolecular Modelling Laboratory The Francis Crick Institute London UK
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- Paul A. Bates
- Biomolecular Modelling Laboratory The Francis Crick Institute London UK
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- Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering Jiangsu University of Technology Changzhou China
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- Bin Liu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering Jiangsu University of Technology Changzhou China
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- Guangbo Yang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering Jiangsu University of Technology Changzhou China
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- Ming Liu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering Jiangsu University of Technology Changzhou China
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- Hang Shi
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering Jiangsu University of Technology Changzhou China
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- Xufeng Lu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering Jiangsu University of Technology Changzhou China
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- Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering Jiangsu University of Technology Changzhou China
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- Raj S. Roy
- Department of Electrical Engineering and Computer Science University of Missouri Columbia Missouri USA
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- Farhan Quadir
- Department of Electrical Engineering and Computer Science University of Missouri Columbia Missouri USA
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- Jian Liu
- Department of Electrical Engineering and Computer Science University of Missouri Columbia Missouri USA
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- Jianlin Cheng
- Department of Electrical Engineering and Computer Science University of Missouri Columbia Missouri USA
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- Anna Antoniak
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Cezary Czaplewski
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Artur Giełdoń
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Mateusz Kogut
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Agnieszka G. Lipska
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Adam Liwo
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Emilia A. Lubecka
- Faculty of Electronics, Telecommunications and Informatics Gdansk University of Technology Gdansk Poland
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- Martyna Maszota‐Zieleniak
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Adam K. Sieradzan
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Rafał Ślusarz
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Patryk A. Wesołowski
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Karolina Zięba
- Faculty of Chemistry University of Gdansk Gdansk Poland
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- Carlos A. Del Carpio Muñoz
- Graduate School of Medical Sciences Nagoya City University Nagoya Japan
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- Eiichiro Ichiishi
- International University of Health and Welfare Hospital (IUHW Hospital) Nasushiobara City Japan
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- Ameya Harmalkar
- Chemical and Biomolecular Engineering Johns Hopkins University Baltimore Maryland USA
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- Jeffrey J. Gray
- Chemical and Biomolecular Engineering Johns Hopkins University Baltimore Maryland USA
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- Alexandre M. J. J. Bonvin
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Francesco Ambrosetti
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Rodrigo Vargas Honorato
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Zuzana Jandova
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Brian Jiménez‐García
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Panagiotis I. Koukos
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Siri Van Keulen
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Charlotte W. Van Noort
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Manon Réau
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Jorge Roel‐Touris
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University Utrecht The Netherlands
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- Sergei Kotelnikov
- Department of Applied Mathematics and Statistics Stony Brook University Stony Brook New York USA
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- Dzmitry Padhorny
- Department of Applied Mathematics and Statistics Stony Brook University Stony Brook New York USA
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- Kathryn A. Porter
- Department of Biomedical Engineering Boston University Boston Massachusetts USA
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- Andrey Alekseenko
- Department of Applied Mathematics and Statistics Stony Brook University Stony Brook New York USA
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- Mikhail Ignatov
- Department of Applied Mathematics and Statistics Stony Brook University Stony Brook New York USA
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- Israel Desta
- Department of Biomedical Engineering Boston University Boston Massachusetts USA
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- Ryota Ashizawa
- Department of Applied Mathematics and Statistics Stony Brook University Stony Brook New York USA
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- Zhuyezi Sun
- Department of Biomedical Engineering Boston University Boston Massachusetts USA
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- Usman Ghani
- Department of Biomedical Engineering Boston University Boston Massachusetts USA
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- Nasser Hashemi
- Department of Biomedical Engineering Boston University Boston Massachusetts USA
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- Sandor Vajda
- Department of Biomedical Engineering Boston University Boston Massachusetts USA
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- Dima Kozakov
- Department of Applied Mathematics and Statistics Stony Brook University Stony Brook New York USA
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- Mireia Rosell
- Instituto de Ciencias de la Vid y del Vino (ICVV) CSIC – Universidad de la Rioja – Gobierno de La Rioja Logrono Spain
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- Luis A. Rodríguez‐Lumbreras
- Instituto de Ciencias de la Vid y del Vino (ICVV) CSIC – Universidad de la Rioja – Gobierno de La Rioja Logrono Spain
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- Juan Fernandez‐Recio
- Instituto de Ciencias de la Vid y del Vino (ICVV) CSIC – Universidad de la Rioja – Gobierno de La Rioja Logrono Spain
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- Agnieszka Karczynska
- Université Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK Grenoble France
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- Sergei Grudinin
- Université Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK Grenoble France
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- Yumeng Yan
- School of Physics Huazhong University of Science and Technology Wuhan China
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- Hao Li
- School of Physics Huazhong University of Science and Technology Wuhan China
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- Peicong Lin
- School of Physics Huazhong University of Science and Technology Wuhan China
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- Sheng‐You Huang
- School of Physics Huazhong University of Science and Technology Wuhan China
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- Charles Christoffer
- Department of Computer Science Purdue University West Lafayette Indiana USA
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- Genki Terashi
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
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- Jacob Verburgt
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
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- Daipayan Sarkar
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
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- Tunde Aderinwale
- Department of Computer Science Purdue University West Lafayette Indiana USA
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- Xiao Wang
- Department of Computer Science Purdue University West Lafayette Indiana USA
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- Daisuke Kihara
- Department of Computer Science Purdue University West Lafayette Indiana USA
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- Tsukasa Nakamura
- Graduate School of Information Sciences Tohoku University Sendai Miyagi Japan
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- Yuya Hanazono
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology Tokai Ibaraki Japan
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- Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research Rockville Maryland USA
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- Johnathan D. Guest
- University of Maryland Institute for Bioscience and Biotechnology Research Rockville Maryland USA
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- Rui Yin
- University of Maryland Institute for Bioscience and Biotechnology Research Rockville Maryland USA
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- Ghazaleh Taherzadeh
- University of Maryland Institute for Bioscience and Biotechnology Research Rockville Maryland USA
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- Brian G. Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research Rockville Maryland USA
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- Didier Barradas‐Bautista
- King Abdullah University of Science and Technology Thuwal Saudi Arabia
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- Zhen Cao
- King Abdullah University of Science and Technology Thuwal Saudi Arabia
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- Luigi Cavallo
- King Abdullah University of Science and Technology Thuwal Saudi Arabia
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- Romina Oliva
- University of Naples “Parthenope” Napoli Italy
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- Yuanfei Sun
- Department of Electrical and Computer Engineering Texas A&M University Texas USA
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- Shaowen Zhu
- Department of Electrical and Computer Engineering Texas A&M University Texas USA
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- Yang Shen
- Department of Electrical and Computer Engineering Texas A&M University Texas USA
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- Taeyong Park
- Department of Chemistry Seoul National University Seoul Republic of Korea
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- Hyeonuk Woo
- Department of Chemistry Seoul National University Seoul Republic of Korea
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- Jinsol Yang
- Department of Chemistry Seoul National University Seoul Republic of Korea
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- Sohee Kwon
- Department of Chemistry Seoul National University Seoul Republic of Korea
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- Jonghun Won
- Department of Chemistry Seoul National University Seoul Republic of Korea
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- Chaok Seok
- Department of Chemistry Seoul National University Seoul Republic of Korea
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- Yasuomi Kiyota
- School of Pharmacy Kitasato University Minato‐ku Tokyo Japan
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- Shinpei Kobayashi
- School of Pharmacy Kitasato University Minato‐ku Tokyo Japan
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- Yoshiki Harada
- School of Pharmacy Kitasato University Minato‐ku Tokyo Japan
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- Mayuko Takeda‐Shitaka
- School of Pharmacy Kitasato University Minato‐ku Tokyo Japan
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- Petras J. Kundrotas
- Computational Biology Program and Department of Molecular Biosciences University of Kansas Lawrence Kansas USA
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- Amar Singh
- Computational Biology Program and Department of Molecular Biosciences University of Kansas Lawrence Kansas USA
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- Ilya A. Vakser
- Computational Biology Program and Department of Molecular Biosciences University of Kansas Lawrence Kansas USA
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- Justas Dapkūnas
- Institute of Biotechnology, Life Sciences Center Vilnius University Vilnius Lithuania
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- Kliment Olechnovič
- Institute of Biotechnology, Life Sciences Center Vilnius University Vilnius Lithuania
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- Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center Vilnius University Vilnius Lithuania
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- Rui Duan
- Dalton Cardiovascular Research Center University of Missouri Columbia Missouri USA
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- Liming Qiu
- Dalton Cardiovascular Research Center University of Missouri Columbia Missouri USA
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- Xianjin Xu
- Dalton Cardiovascular Research Center University of Missouri Columbia Missouri USA
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- Shuang Zhang
- Dalton Cardiovascular Research Center University of Missouri Columbia Missouri USA
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- Xiaoqin Zou
- Institute for Data Science and Informatics University of Missouri Columbia Missouri USA
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- Shoshana J. Wodak
- Center for Structural Biology VIB‐VUB Brussels Belgium
Description
<jats:title>Abstract</jats:title><jats:p>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.</jats:p>
Journal
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- Proteins: Structure, Function, and Bioinformatics
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Proteins: Structure, Function, and Bioinformatics 89 (12), 1800-1823, 2021-09-13
Wiley
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Details 詳細情報について
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- CRID
- 1360857593724032512
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- ISSN
- 10970134
- 08873585
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- Data Source
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- Crossref
- KAKEN