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

Marc Lensink (1) , Guillaume Brysbaert (1) , Théo Mauri (1) , Nurul Nadzirin (2) , Sameer Velankar (2) , Raphael Chaleil (3) , Tereza Clarence (3) , Paul Bates (3) , Ren Kong (4) , Bin Liu (4) , Guangbo Yang (4) , Ming Liu (4) , Hang Shi (4) , Xufeng Lu (4) , Shan Chang (4) , Raj Roy (5) , Farhan Quadir (5) , Jian Liu (5) , Jianlin Cheng (5, 6) , Anna Antoniak (7) , Cezary Czaplewski (7) , Artur Giełdoń (7) , Mateusz Kogut (7) , Agnieszka Lipska (7) , Adam Liwo (7) , Emilia Lubecka (8) , Martyna Maszota‐zieleniak (7) , Adam Sieradzan (7) , Rafał Ślusarz (7) , Patryk Wesołowski (7, 9) , Karolina Zięba (7) , Carlos del Carpio Muñoz (10) , Eiichiro Ichiishi (11) , Ameya Harmalkar (12) , Jeffrey Gray (12) , Alexandre Bonvin (13) , Francesco Ambrosetti (13) , Rodrigo Vargas Honorato (13) , Zuzana Jandova (13) , Brian Jiménez‐garcía (13) , Panagiotis Koukos (13) , Siri van Keulen (13) , Charlotte van Noort (13) , Manon Réau (13) , Jorge Roel‐touris (13) , Sergei Kotelnikov (14, 15) , Dzmitry Padhorny (14) , Kathryn Porter (16) , Andrey Alekseenko (14, 17) , Mikhail Ignatov (16) , Israel Desta (16) , Ryota Ashizawa (14) , Zhuyezi Sun (16) , Usman Ghani (16) , Nasser Hashemi (16) , Sandor Vajda (16) , Dima Kozakov (14) , Mireia Rosell (18, 19) , Luis Rodríguez‐lumbreras (19, 18) , Juan Fernandez‐recio (19, 18) , Agnieszka Karczynska (20) , Sergei Grudinin (20, 20) , Yumeng Yan (21) , Hao Li (21) , Peicong Lin (21) , Sheng‐you Huang (21) , Charles Christoffer (22) , Genki Terashi (22) , Jacob Verburgt (22) , Daipayan Sarkar (22) , Tunde Aderinwale (22) , Xiao Wang (22) , Daisuke Kihara (22) , Tsukasa Nakamura (23) , Yuya Hanazono (24) , Ragul Gowthaman (25) , Johnathan Guest (25) , Rui Yin (25) , Ghazaleh Taherzadeh (25) , Brian Pierce (25) , Didier Barradas‐bautista (26) , Zhen Cao (26) , Luigi Cavallo (26) , Romina Oliva (27) , Yuanfei Sun (28) , Shaowen Zhu (28) , Yang Shen (28) , Taeyong Park (29) , Hyeonuk Woo (29) , Jinsol Yang (29) , Sohee Kwon (29) , Jonghun Won (29) , Chaok Seok (29) , Yasuomi Kiyota (30) , Shinpei Kobayashi (30) , Yoshiki Harada (30) , Mayuko Takeda‐shitaka (30) , Petras Kundrotas (31) , Amar Singh (31) , Ilya Vakser (31) , Justas Dapkūnas (32) , Kliment Olechnovič (32) , Česlovas Venclovas (32) , Rui Duan (33) , Liming Qiu (33) , Xianjin Xu (33) , Shuang Zhang (33) , Xiaoqin Zou (33) , Shoshana Wodak (34)

1 UGSF - Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576
2 EMBL-EBI - European Bioinformatics Institute [Hinxton]
3 Biomolecular Modelling Laboratory [London]
4 Jiangsu University of Technology [Changzhou]
5 EECS - Department of Electrical Engineering and Computer Science [Columbia]
6 Institute for Data Science and Informatics [Columbia]
7 UG - University of Gdańsk
8 ETI - Faculty of Electronics, Telecommunications and Informatics [GUT Gdańsk]
9 Medical University of Gdańsk
10 Graduate School of Medical Sciences [Nagoya]
11 IUHW Hospital - International University of Health and Welfare Hospital
12 Department of Chemical and Biomolecular Engineering [Baltimore]
13 Bijvoet Center of Biomolecular Research [Utrecht]
14 SBU - Stony Brook University [SUNY]
15 Innopolis University
16 BU - Boston University [Boston]
17 RAS - Russian Academy of Sciences [Moscow]
18 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
19 UR - Universidad de La Rioja
20 DAO - Données, Apprentissage et Optimisation
21 HUST - Huazhong University of Science and Technology [Wuhan]
22 IUPUI - Indiana University - Purdue University Indianapolis
23 Graduate School of Information Sciences [Sendaï]
24 QST - National Institutes for Quantum and Radiological Science and Technology
25 University of Maryland [Baltimore]
26 KAUST - King Abdullah University of Science and Technology [Saudi Arabia]
27 University of Naples Federico II = Università degli studi di Napoli Federico II
28 Texas A&M University [Galveston]
29 SNU - Seoul National University [Seoul]
30 Kitasato University
31 KU - University of Kansas [Lawrence]
32 Vilnius University [Vilnius]
33 Mizzou - University of Missouri [Columbia]
34 VIB-VUB Center for Structural Biology [Bruxelles]

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.

Mots clés: CAPRI; CASP; oligomeric state; blind prediction; protein-protein interaction; protein complexes; protein assemblies; template-based modeling; docking; protein docking

Domaines: Sciences du Vivant [q-bio]

Marc Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, et al.. Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment. Proteins - Structure, Function and Bioinformatics, 2021, 89 (12), pp.1800-1823. ⟨10.1002/prot.26222⟩. ⟨hal-03448743⟩