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

Marc Lensink 1 Guillaume Brysbaert 1 Nurul Nadzirin 2 Sameer Velankar 2 Raphaël A.G. Chaleil 3 Tereza Gerguri 3 Paul Bates 4 Elodie Laine 5 Alessandra Carbone 6 Sergei Grudinin 7 Ren Kong 8 Ran‐ran Liu 8 Xi‐ming Xu 8 Hang Shi 8 Shan Chang 8 Miriam Eisenstein 9 Agnieszka Karczynska 10 Cezary Czaplewski 11 Emilia Lubecka 10 Agnieszka Lipska 10 Paweł Krupa 12 Magdalena Mozolewska 13 Łukasz Golon 10 Sergey Samsonov 10 Adam Liwo 11 Silvia Crivelli 14 Guillaume Pagès 7 Mikhail Karasikov 15, 7 Maria Kadukova 15, 7 Yumeng Yan 16 Sheng‐you Huang 16 Mireia Rosell 17 Luis Angel Rodríguez‐lumbreras 17 Miguel Romero‐durana 17 Lucía Díaz‐bueno 17 Juan Fernandez‐recio 17 Charles Christoffer 18 Genki Terashi 19 Woong‐hee Shin 18 Tunde Aderinwale 18 Sai Raghavendra Maddhuri Venkata Subram 18 Daisuke Kihara 18 Dima Kozakov 20 Sandor Vajda 21 Kathyn Porter 21 Dzmitry Padhorny 21 Israel Desta 21 Dmitri Beglov 21 Mikhail Ignatov 20 Sergey Kotelnikov 20 Iain Moal 17 David Ritchie 22 Isaure Chauvot de Beauchêne 23, 22 Bernard Maigret 22 Marie-Dominique Devignes 22 Maria Elisa Ruiz Echartea 22 Didier Barradas‐bautista 24 Zhen Cao 24 Luigi Cavallo 24 Romina Oliva 25 Yue Cao 24 Yang Shen 26 Minkyung Baek 27 Taeyong Park 27 Hyeonuk Woo 27 Chaok Seok 28 Merav Braitbard 29 Lirane Bitton 29 Dina Scheidman‐duhovny 29 Justas Dapkūnas 30 Kliment Olechnovič 30 Česlovas Venclovas 30 Petras Kundrotas 31 Saveliy Belkin 32 Devlina Chakravarty 32 Varsha Badal 32 Ilya Vakser 33 Thom Vreven 34 Sweta Vangaveti 34 Tyler Borrman 35 Zhiping Weng 34 Johnathan Guest 36 Ragul Gowthaman 36 Brian Pierce 36 Xianjin Xu 37 Rui Duan 38 Liming Qiu 39 Jie Hou 38 Benjamin Ryan Merideth 38 Zhiwei Ma 39 Jianlin Cheng 38 Xiaoqin Zou 40 Panos Koukos 41 Jorge Roel‐touris 41 Francesco Ambrosetti 41 Cunliang Geng 42 Jörg Schaarschmidt 41 Mikael Trellet 43 Adrien S.J. Melquiond 41 Li Xue 44 Brian Jiménez‐garcía 41 Charlotte Noort 41 Rodrigo Honorato 41 Alexandre M.J.J. Bonvin 41 Shoshana Wodak 45
7 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, Grenoble INP - Institut polytechnique de Grenoble - Grenoble Institute of Technology, LJK - Laboratoire Jean Kuntzmann
22 CAPSID - Computational Algorithms for Protein Structures and Interactions
Inria Nancy - Grand Est, LORIA - AIS - Department of Complex Systems, Artificial Intelligence & Robotics
Abstract : 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 ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~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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Marc Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphaël A.G. Chaleil, et al.. Blind prediction of homo‐ and hetero‐ protein complexes: The CASP13‐CAPRI experiment. Proteins - Structure, Function and Bioinformatics, Wiley, 2019, 87 (12), pp.1200-1221. ⟨10.1002/prot.25838⟩. ⟨hal-02320974⟩

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