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

Marc Lensink 1 Guillaume Brysbaert 2 Nurul Nadzirin 3 Sameer Velankar 3 Raphaël A.G. Chaleil 4 Tereza Gerguri 4 Paul Bates 5 Elodie Laine 6 Alessandra Carbone 7 Sergei Grudinin 8 Ren Kong 9 Ran‐ran Liu 9 Xi‐ming Xu 9 Hang Shi 9 Shan Chang 9 Miriam Eisenstein 10 Agnieszka Karczynska 11 Cezary Czaplewski 12 Emilia Lubecka 11 Agnieszka Lipska 11 Paweł Krupa 13 Magdalena Mozolewska 14 Łukasz Golon 11 Sergey Samsonov 11 Adam Liwo 12 Silvia Crivelli 15 Guillaume Pagès 8 Mikhail Karasikov 16, 8 Maria Kadukova 16, 8 Yumeng Yan 17 Sheng‐you Huang 17 Mireia Rosell 18 Luis Angel Rodríguez‐lumbreras 18 Miguel Romero‐durana 18 Lucía Díaz‐bueno 18 Juan Fernandez‐recio 18 Charles Christoffer 19 Genki Terashi 20 Woong‐hee Shin 19 Tunde Aderinwale 19 Sai Raghavendra Maddhuri Venkata Subram 19 Daisuke Kihara 19 Dima Kozakov 21 Sandor Vajda 22 Kathyn Porter 22 Dzmitry Padhorny 22 Israel Desta 22 Dmitri Beglov 22 Mikhail Ignatov 21 Sergey Kotelnikov 21 Iain Moal 18 David Ritchie 23 Isaure Chauvot de Beauchêne 24, 23 Bernard Maigret 23 Maria Elisa Ruiz Echartea 23 Didier Barradas‐bautista 25 Zhen Cao 25 Luigi Cavallo 25 Romina Oliva 26 Yue Cao 25 Yang Shen 27 Minkyung Baek 28 Taeyong Park 28 Hyeonuk Woo 28 Chaok Seok 29 Merav Braitbard 30 Lirane Bitton 30 Dina Scheidman‐duhovny 30 Justas Dapkūnas 31 Kliment Olechnovič 31 Česlovas Venclovas 31 Petras Kundrotas 32 Saveliy Belkin 33 Devlina Chakravarty 33 Varsha Badal 33 Ilya Vakser 34 Thom Vreven 35 Sweta Vangaveti 35 Tyler Borrman 36 Zhiping Weng 35 Johnathan Guest 37 Ragul Gowthaman 37 Brian Pierce 37 Xianjin Xu 38 Rui Duan 39 Liming Qiu 40 Jie Hou 39 Benjamin Ryan Merideth 39 Zhiwei Ma 40 Jianlin Cheng 39 Xiaoqin Zou 41 Panos Koukos 42 Jorge Roel‐touris 42 Francesco Ambrosetti 42 Cunliang Geng 43 Jörg Schaarschmidt 42 Mikael Trellet 44 Adrien S.J. Melquiond 42 Li Xue 45 Brian Jiménez‐garcía 42 Charlotte Noort 42 Rodrigo Honorato 42 Alexandre M.J.J. Bonvin 42 Shoshana Wodak 46
8 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
23 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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https://hal.inria.fr/hal-02320974
Contributor : Sergei Grudinin <>
Submitted on : Sunday, October 20, 2019 - 2:46:56 AM
Last modification on : Thursday, March 26, 2020 - 8:49:37 PM

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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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