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Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment
  • +110
  • Marc Lensink,
  • Guillaume Brysbaert,
  • Nessim Raouraoua,
  • Paul Bates,
  • Marco Giulini,
  • Rodrigo Vargas Honorato,
  • Charlotte van Noort,
  • João Teixeira,
  • Alexandre M.J.J. Bonvin,
  • Ren Kong,
  • Hang Shi,
  • Xufeng Lu,
  • Shan Chang,
  • Jian Liu,
  • Zhiye Guo,
  • Xiao Chen,
  • Alex Morehead,
  • Raj Roy,
  • Tianqi Wu,
  • Nabin Giri,
  • Farhan Quadir,
  • Chen Chen,
  • Jianlin Cheng,
  • Carlos Del Carpio,
  • Eichiro Ichiishi,
  • Luis Ángel Rodríguez-Lumbreras,
  • Juan Fernández-Recio,
  • Ameya Harmalkar,
  • Lee-Shin Chu,
  • Sam Canner,
  • Rituparna Smanta,
  • Jeffrey Gray,
  • Hao Li,
  • Peicong Lin,
  • Jiahua He,
  • Huanyu Tao,
  • Shengyou Huang,
  • Jorge Roel,
  • Brian Jimenez-Garcia,
  • Charles Christoffer,
  • Anika Jain J,
  • Yuki Kagaya,
  • Harini Kannan,
  • Tsukasa Nakamura,
  • Genki Terashi,
  • Jacob Verburgt,
  • Yuanyuan Zhang,
  • Zicong Zhang,
  • Hayato Fujuta,
  • Masakazu Sekijima,
  • Daisuke Kihara,
  • Omeir Khan,
  • Sergei Kotelnikov,
  • Usman Ghani,
  • Dzmitry Padhorny,
  • Dmitri Beglov,
  • Sandor Vajda,
  • Dima Kozakov,
  • Surendra Negi S,
  • Tiziana Ricciardelli,
  • Didier Barradas-Bautista,
  • Zhen Cao,
  • Mohit Chawla,
  • Luigi Cavallo,
  • Romina Oliva,
  • Rui Yin,
  • Melyssa Cheung,
  • Johnathan Guest,
  • Jessica Lee,
  • Brian Pierce,
  • Ben Shor,
  • Tomer Cohen,
  • Matan Halfon,
  • Dina Schneidman-Duhovny,
  • Shaowen Zhu,
  • Rujie Yin,
  • Yuanfei Sun,
  • Yang Shen,
  • Martyna Maszota-Zieleniak,
  • Krzysztof Bojarski K,
  • Emilia Lubecka,
  • Mateusz Marcisz,
  • Annemarie Danielsson,
  • Lukasz Dziadek,
  • Margrethe Gaardlos,
  • Artur Giełdoń,
  • Jozef Liwo,
  • Sergey Samsonov,
  • Rafal Slusarz,
  • Karolina Zieba,
  • Adam Sieradzan,
  • Cezary Czaplewski ,
  • Shinpei Kobayashi,
  • Yuta Miyakawa,
  • Yasuomi Kiyota,
  • Mayuko Takeda-Shitaka,
  • Kliment Olechnovič,
  • Lukas Valančauskas,
  • Justas Dapkūnas,
  • Ceslovas Venclovas,
  • Björn Wallner,
  • Lin Yang,
  • Chengyu Hou,
  • Xiaodong He,
  • Shuai Guo,
  • Shenda Jiang,
  • Xiaoliang Ma,
  • Rui Duan,
  • Liming Qiu,
  • Xianjin Xu,
  • Xiaoqin Zou,
  • Sameer Velankar,
  • Shoshana Wodak J
Marc Lensink
Unite de Glycobiologie Structurale et Fonctionnelle

Corresponding Author:marc.lensink@univ-lille.fr

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Guillaume Brysbaert
Unite de Glycobiologie Structurale et Fonctionnelle
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Nessim Raouraoua
Unite de Glycobiologie Structurale et Fonctionnelle
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Paul Bates
The Francis Crick Institute
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Marco Giulini
Universiteit Utrecht Departement Scheikunde
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Rodrigo Vargas Honorato
Universiteit Utrecht Departement Scheikunde
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Charlotte van Noort
Universiteit Utrecht Departement Scheikunde
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João Teixeira
Universiteit Utrecht Departement Scheikunde
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Alexandre M.J.J. Bonvin
Universiteit Utrecht Departement Scheikunde
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Ren Kong
Jiangsu University School of Electrical and Information Engineering
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Hang Shi
Jiangsu University School of Electrical and Information Engineering
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Xufeng Lu
Jiangsu University School of Electrical and Information Engineering
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Shan Chang
Jiangsu University School of Electrical and Information Engineering
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Jian Liu
University of Missouri
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Zhiye Guo
University of Missouri
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Xiao Chen
University of Missouri
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Alex Morehead
University of Missouri
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Raj Roy
University of Missouri
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Tianqi Wu
University of Missouri
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Nabin Giri
University of Missouri
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Farhan Quadir
University of Missouri
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Chen Chen
University of Missouri
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Jianlin Cheng
University of Missouri
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Carlos Del Carpio
Fukushimuta Hospital
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Eichiro Ichiishi
International University of Health and Welfare (IUHV Hospital
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Luis Ángel Rodríguez-Lumbreras
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Juan Fernández-Recio
Universidad Internacional de la Rioja - Campus de Logrono
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Ameya Harmalkar
Johns Hopkins University Department of Chemical and Biomolecular Engineering
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Lee-Shin Chu
Johns Hopkins University Department of Chemical and Biomolecular Engineering
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Sam Canner
Johns Hopkins University
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Rituparna Smanta
Johns Hopkins University Department of Chemical and Biomolecular Engineering
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Jeffrey Gray
Johns Hopkins University Department of Chemical and Biomolecular Engineering
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Hao Li
Huazhong University of Science and Technology School of Physics
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Peicong Lin
Huazhong University of Science and Technology School of Physics
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Jiahua He
Huazhong University of Science and Technology School of Physics
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Huanyu Tao
Huazhong University of Science and Technology School of Physics
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Shengyou Huang
Huazhong University of Science and Technology School of Physics
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Jorge Roel
Institut de Biologia Molecular de Barcelona
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Brian Jimenez-Garcia
Zymvol Biomodeling
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Charles Christoffer
Purdue University
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Anika Jain J
Purdue University Department of Biological Sciences
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Yuki Kagaya
Purdue University Department of Biological Sciences
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Harini Kannan
Purdue University Department of Biological Sciences
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Tsukasa Nakamura
Purdue University Department of Biological Sciences
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Genki Terashi
Purdue University Department of Biological Sciences
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Jacob Verburgt
Purdue University Department of Biological Sciences
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Yuanyuan Zhang
Purdue University
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Zicong Zhang
Purdue University
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Hayato Fujuta
Tokyo Institute of Technology
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Masakazu Sekijima
Tokyo Institute of Technology
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Daisuke Kihara
Purdue University
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Omeir Khan
Boston University
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Sergei Kotelnikov
Stony Brook University
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Usman Ghani
Boston University
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Dzmitry Padhorny
Stony Brook University
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Dmitri Beglov
Boston University
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Sandor Vajda
Boston University
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Dima Kozakov
Stony Brook University
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Surendra Negi S
The University of Texas Medical Branch at Galveston Sealy Center for Structural Biology and Molecular Biophysics
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Tiziana Ricciardelli
The KAUST School
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Didier Barradas-Bautista
The KAUST School
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Zhen Cao
The KAUST School
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Mohit Chawla
The KAUST School
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Luigi Cavallo
The KAUST School
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Romina Oliva
Universita degli Studi di Napoli Parthenope
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Rui Yin
Institute for Bioscience and Biotechnology Research Shady Grove
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Melyssa Cheung
Institute for Bioscience and Biotechnology Research Shady Grove
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Johnathan Guest
Institute for Bioscience and Biotechnology Research Shady Grove
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Jessica Lee
Institute for Bioscience and Biotechnology Research Shady Grove
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Brian Pierce
Institute for Bioscience and Biotechnology Research Shady Grove
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Ben Shor
Hebrew University of Jeruslaem Rachel and Selim Benin School of Computer Science and Engineering
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Tomer Cohen
Hebrew University of Jeruslaem Rachel and Selim Benin School of Computer Science and Engineering
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Matan Halfon
Hebrew University of Jeruslaem Rachel and Selim Benin School of Computer Science and Engineering
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Dina Schneidman-Duhovny
Hebrew University of Jeruslaem Rachel and Selim Benin School of Computer Science and Engineering
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Shaowen Zhu
Texas A&M University Department of Electrical and Computer Engineering
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Rujie Yin
Texas A&M University Department of Electrical and Computer Engineering
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Yuanfei Sun
Texas A&M University Department of Electrical and Computer Engineering
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Yang Shen
Texas A&M University Department of Electrical and Computer Engineering
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Martyna Maszota-Zieleniak
Uniwersytet Gdanski Wydzial Chemii
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Krzysztof Bojarski K
Technical University of Gdansk
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Emilia Lubecka
Technical University of Gdansk
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Mateusz Marcisz
Uniwersytet Gdanski Wydzial Chemii
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Annemarie Danielsson
Uniwersytet Gdanski Wydzial Chemii
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Lukasz Dziadek
Uniwersytet Gdanski Wydzial Chemii
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Margrethe Gaardlos
Uniwersytet Gdanski Wydzial Chemii
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Artur Giełdoń
Uniwersytet Gdanski Wydzial Chemii
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Jozef Liwo
Uniwersytet Gdanski Wydzial Chemii
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Sergey Samsonov
Uniwersytet Gdanski Wydzial Chemii
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Rafal Slusarz
Uniwersytet Gdanski Wydzial Chemii
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Karolina Zieba
Uniwersytet Gdanski Wydzial Chemii
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Adam Sieradzan
Uniwersytet Gdanski Wydzial Chemii
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Cezary Czaplewski
Uniwersytet Gdanski Wydzial Chemii
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Shinpei Kobayashi
Kitasato University
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Yuta Miyakawa
Kitasato University
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Yasuomi Kiyota
Kitasato University
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Mayuko Takeda-Shitaka
Kitasato University
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Kliment Olechnovič
Vilnius University
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Lukas Valančauskas
Vilnius University
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Justas Dapkūnas
Vilnius University
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Ceslovas Venclovas
Vilnius University
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Björn Wallner
Linkopings universitet Institutionen for fysik kemi och biologi
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Lin Yang
Harbin Institute of Technology National Key Laboratory of Science and Technology on Advanced Composites in Special Environments
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Chengyu Hou
Harbin Institute of Technology School of Electronics and Information Engineering
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Xiaodong He
Harbin Institute of Technology National Key Laboratory of Science and Technology on Advanced Composites in Special Environments
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Shuai Guo
Harbin Institute of Technology National Key Laboratory of Science and Technology on Advanced Composites in Special Environments
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Shenda Jiang
Harbin Institute of Technology National Key Laboratory of Science and Technology on Advanced Composites in Special Environments
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Xiaoliang Ma
Harbin Institute of Technology National Key Laboratory of Science and Technology on Advanced Composites in Special Environments
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Rui Duan
University of Missouri Dalton Cardiovascular Research Center
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Liming Qiu
University of Missouri Dalton Cardiovascular Research Center
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Xianjin Xu
University of Missouri Dalton Cardiovascular Research Center
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Xiaoqin Zou
University of Missouri Dalton Cardiovascular Research Center
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Sameer Velankar
European Bioinformatics Institute
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Shoshana Wodak J
Structural Biology Research Center
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Abstract

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homo-dimers, 3 homo-trimers, 13 hetero-dimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their 5 best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% for the targets compared to 8% two years earlier, a remarkable improvement resulting from the wide use of the AlphaFold2 and AlphaFold-Multimer software. Creative use was made of the deep learning inference engines affording the sampling of a much larger number of models and enriching the multiple sequence alignments with sequences from various sources. Wide use was also made of the AlphaFold confidence metrics to rank models, permitting top performing groups to exceed the results of the public AlphaFold-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
08 Jul 2023Submitted to PROTEINS: Structure, Function, and Bioinformatics
09 Jul 2023Submission Checks Completed
09 Jul 2023Assigned to Editor
09 Jul 2023Review(s) Completed, Editorial Evaluation Pending
10 Jul 2023Reviewer(s) Assigned
14 Aug 2023Editorial Decision: Revise Major
19 Sep 20231st Revision Received
22 Sep 2023Submission Checks Completed
22 Sep 2023Assigned to Editor
22 Sep 2023Review(s) Completed, Editorial Evaluation Pending
22 Sep 2023Reviewer(s) Assigned
28 Sep 2023Editorial Decision: Accept