Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Marc F. Lensink; Guillaume Brysbaert; Nurul Nadzirin; Sameer Velankar; Raphael A. G. Chaleil; Tereza Gerguri; Paul A. Bates; Elodie Laine; Alessandra Carbone; Sergei Grudinin; Ren Kong; Ran-Ran Liu; Xi-Ming Xu; Hang Shi; Shan Chang; Miriam Eisenstein; Agnieszka Karczynska; Cezary Czaplewski; Emilia Lubecka; Agnieszka Lipska; Pawel Krupa; Magdalena Mozolewska; Lukasz Golon; Sergey Samsonov; Adam Liwo; Silvia Crivelli; Guillaume Pages; Mikhail Karasikov; Maria Kadukova; Yumeng Yan; Sheng-You Huang; Mireia Rosell; Luis A. Rodriguez-Lumbreras; Miguel Romero-Durana; Lucia Diaz-Bueno; Juan Fernandez-Recio; Charles Christoffer; Genki Terashi; Woong-Hee Shin; Tunde Aderinwale; Sai Raghavendra Maddhuri Venkata Subraman; Daisuke Kihara; Dima Kozakov; Sandor Vajda; Kathryn Porter; Dzmitry Padhorny; Israel Desta; Dmitri Beglov; Mikhail Ignatov; Sergey Kotelnikov; Iain H. Moal; David W. Ritchie; Isaure Chauvot de Beauchene; Bernard Maigret; Marie-Dominique Devignes; Maria E. Ruiz Echartea; Didier Barradas-Bautista; Zhen Cao; Luigi Cavallo; Romina Oliva; Yue Cao; Yang Shen; Minkyung Baek; Taeyong Park; Hyeonuk Woo; Chaok Seok; Merav Braitbard; Lirane Bitton; Dina Scheidman-Duhovny; Justas Dapkunas; Kliment Olechnovic; Ceslovas Venclovas; Petras J. Kundrotas; Saveliy Belkin; Devlina Chakravarty; Varsha D. Badal; Ilya A. Vakser; Thom Vreven; Sweta Vangaveti; Tyler Borrman; Zhiping Weng; Johnathan D. Guest; Ragul Gowthaman; Brian G. Pierce; Xianjin Xu; Rui Duan; Liming Qiu; Jie Hou; Benjamin Ryan Merideth; Zhiwei Ma; Jianlin Cheng; Xiaoqin Zou; Panos I. Koukos; Jorge Roel-Touris; Francesco Ambrosetti; Cunliang Geng; Jorg Schaarschmidt; Mikael E. Trellet; Adrien S. J. Melquiond; Li Xue; Brian Jimenez-Garcia; Charlotte W. van Noort; Rodrigo V. Honorato; Alexandre M. J. J. Bonvin; Shoshana J. Wodak

doi:10.1002/prot.25838

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Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Journal article

Peer reviewed

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Marc F. Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphael A. G. Chaleil, Tereza Gerguri, Paul A. Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, …

Proteins, structure, function, and bioinformatics, Vol.87(12), pp.1200-1221

12/2019

DOI: https://doi.org/10.1002/prot.25838

PMCID: 7274794

PMID: 31612567

Abstract

Biochemistry & Molecular Biology

Biophysics

Life Sciences & Biomedicine

Science & Technology

We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved "ab-initio" docking of subunit models derived from distantly related templates. A total of similar to 30 CAPRI groups, including 9 automatic servers, submitted on average similar to 2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting similar to 170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance "gap" was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.

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Title: Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment
Creators - without role: Marc F. Lensink - Unité de Glycobiologie Structurale et Fonctionnelle
Guillaume Brysbaert - Unité de Glycobiologie Structurale et Fonctionnelle
Nurul Nadzirin - European Bioinformatics Institute
Sameer Velankar - European Bioinformatics Institute
Raphael A. G. Chaleil - The Francis Crick Institute
Tereza Gerguri - The Francis Crick Institute
Paul A. Bates - The Francis Crick Institute
Elodie Laine - Laboratory of Computational and Quantitative Biology
Alessandra Carbone - Laboratory of Computational and Quantitative Biology
Sergei Grudinin - Université Grenoble Alpes
Ren Kong - Jiangsu University of Technology
Ran-Ran Liu - Jiangsu University of Technology
Xi-Ming Xu - Jiangsu University of Technology
Hang Shi - Jiangsu University of Technology
Shan Chang - Jiangsu University of Technology
Miriam Eisenstein - Weizmann Institute of Science
Agnieszka Karczynska - University of Gdańsk
Cezary Czaplewski - University of Gdańsk
Emilia Lubecka - University of Gdańsk
Agnieszka Lipska - University of Gdańsk
Pawel Krupa - Polish Acad Sci, Inst Phys, Warsaw, Poland
Magdalena Mozolewska - Polish Academy of Sciences
Lukasz Golon - University of Gdańsk
Sergey Samsonov - University of Gdańsk
Adam Liwo - University of Gdańsk
Silvia Crivelli - University of California, Davis
Guillaume Pages - Université Grenoble Alpes
Mikhail Karasikov - ETH Zurich
Maria Kadukova - Université Grenoble Alpes
Yumeng Yan - Huazhong University of Science and Technology
Sheng-You Huang - Huazhong University of Science and Technology
Mireia Rosell - Barcelona Supercomputing Center
Luis A. Rodriguez-Lumbreras - Barcelona Supercomputing Center
Miguel Romero-Durana - Barcelona Supercomputing Center
Lucia Diaz-Bueno - BSC, Barcelona, Spain
Juan Fernandez-Recio - Barcelona Supercomputing Center
Charles Christoffer - Purdue University West Lafayette
Genki Terashi - Purdue University West Lafayette
Woong-Hee Shin - Purdue University West Lafayette
Tunde Aderinwale - Purdue University West Lafayette
Sai Raghavendra Maddhuri Venkata Subraman - Purdue Univ, Dept Comp Sci, W Lafayette, IN 47907 USA
Daisuke Kihara - Purdue University West Lafayette
Dima Kozakov - Stony Brook University
Sandor Vajda - Boston University
Kathryn Porter - Boston University
Dzmitry Padhorny - Stony Brook University
Israel Desta - Boston University
Dmitri Beglov - Boston University
Mikhail Ignatov - Stony Brook University
Sergey Kotelnikov - Moscow Institute of Physics and Technology (Russia, Dolgoprudnyy) - MIPT
Iain H. Moal - European Bioinformatics Institute
David W. Ritchie - Université de Lorraine
Isaure Chauvot de Beauchene - Université de Lorraine
Bernard Maigret - Université de Lorraine
Marie-Dominique Devignes - Université de Lorraine
Maria E. Ruiz Echartea - Université de Lorraine
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
Yue Cao - Texas A&M University
Yang Shen - Texas A&M University
Minkyung Baek - Seoul National University
Taeyong Park - Seoul Natl Univ, Dept Chem, Seoul, South Korea
Hyeonuk Woo - Seoul National University
Chaok Seok - Seoul National University
Merav Braitbard - Hebrew University of Jerusalem
Lirane Bitton - Hebrew University of Jerusalem
Dina Scheidman-Duhovny - Hebrew University of Jerusalem
Justas Dapkunas - Vilnius University
Kliment Olechnovic - Vilnius University
Ceslovas Venclovas - Vilnius University
Petras J. Kundrotas - University of Kansas
Saveliy Belkin - University of Kansas
Devlina Chakravarty - University of Kansas
Varsha D. Badal - University of Kansas
Ilya A. Vakser - University of Kansas
Thom Vreven - University of Massachusetts Chan Medical School
Sweta Vangaveti - University of Massachusetts Chan Medical School
Tyler Borrman - University of Massachusetts Chan Medical School
Zhiping Weng - University of Massachusetts Chan Medical School
Johnathan D. Guest - Advanced Bioscience Laboratories
Ragul Gowthaman - Advanced Bioscience Laboratories
Brian G. Pierce - Advanced Bioscience Laboratories
Xianjin Xu - University of Missouri
Rui Duan - University of Missouri
Liming Qiu - University of Missouri
Jie Hou - University of Missouri
Benjamin Ryan Merideth - University of Missouri
Zhiwei Ma - University of Missouri
Jianlin Cheng - University of Missouri
Xiaoqin Zou - University of Missouri
Panos I. Koukos - Utrecht University
Jorge Roel-Touris - Utrecht University
Francesco Ambrosetti - Utrecht University
Cunliang Geng - Utrecht University
Jorg Schaarschmidt - Utrecht University
Mikael E. Trellet - Utrecht University
Adrien S. J. Melquiond - Univ Utrecht, Fac Sci, Dept Chem, Computat Struct Biol Grp, Utrecht, Netherlands
Li Xue - Univ Utrecht, Fac Sci, Dept Chem, Computat Struct Biol Grp, Utrecht, Netherlands
Brian Jimenez-Garcia - Univ Utrecht, Fac Sci, Dept Chem, Computat Struct Biol Grp, Utrecht, Netherlands
Charlotte W. van Noort - Univ Utrecht, Fac Sci, Dept Chem, Computat Struct Biol Grp, Utrecht, Netherlands
Rodrigo V. Honorato - Univ Utrecht, Fac Sci, Dept Chem, Computat Struct Biol Grp, Utrecht, Netherlands
Alexandre M. J. J. Bonvin - Univ Utrecht, Fac Sci, Dept Chem, Computat Struct Biol Grp, Utrecht, Netherlands
Shoshana J. Wodak - VUB VIB, Struct Biol Res Ctr, Pleinlaan 2, B-1050 Brussels, Belgium
Publication Details: Proteins, structure, function, and bioinformatics, Vol.87(12), pp.1200-1221
Publisher: Wiley
Number of pages: 22
Grant note: University Parthenope FC001003 / Wellcome Trust FC001003 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) FC001003 / Cancer Research UK S-MIP-17-60 / Lietuvos Mokslo Taryba; Research Council of Lithuania (LMTLT) 675728; 777536; 823830 / H2020 European Institute of Innovation and Technology BIO2016-79930-R / Spanish "Programma Estatal I+D+i" ANR-15-CE11-0029-03 / Agence Nationale de la Recherche; Agence Nationale de la Recherche (ANR) 31670724 / National Natural Science Foundation of China; National Natural Science Foundation of China (NSFC) DBI1565107 / National Science Foundation; National Science Foundation (NSF) R01GM074255; R01GM123055; R35GM124952 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA 718.015.001 / Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Netherlands Organization for Scientific Research (NWO) 2016M3C4A7952630 / National Research Foundation of Korea
Identifiers: 9941412408331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article