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Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Marc F. Lensink 1 Sameer Velankar 2 Andriy Kryshtafovych 3 Shen-You Huang 4, 5 Dina Schneidman-Duhovy 6, 7 Andrej Sali 6 Joan Segura 8 Narcis Fernandez-Fuentes 9 Shruthi Viswanath 10, 11 Ron Elber 10, 12 Sergei Grudinin 13 Petr Popov 14, 13 Emilie Neveu 13 Hasup Lee 15 Minkyung Baek 15 Sangwoo Park 15 Lim Heo 15 Gyu Rie Lee 15 Chaok Seok 15 Sanbo Qin 16 Huan-Xiang Zhou 16 David W. Ritchie 17 Bernard Maigret 17 Marie-Dominique Devignes 17 Anisah Ghoorah 18 Mieczyslaw Torchala 19 Raphaël Chaleil 19 Paul A Bates 19 Efrat Ben-Zeev 20 Miriam Eisenstein 21 Surendra Negi S. 22 Thom Vreven 23 Brian G Pierce 23 Tyler Borrman 23 Jinchao Yu 23 Françoise Ochsenbein 24, 25 Zhiping Weng 23 Raphaël Guérois 24, 25 Anna Vangone João Rodrigues Gydo van Zundert Mehdi Nellen Li Xue Ezgi Karaca Adrien S. J. Melquiond Koen Visscher Panagiotis L Kastritis Alexandre Bonvin Xianjin Xu 26 Liming Qiu 26 Chengfei Yan 27, 26 Jilong Li 28 Zhiwei Ma 26, 27 Jianlin Cheng 28, 29 Xiaoqin Zou 26, 27, 29, 30 Yang Sheng 31 Lenna Peterson 32 Hyung-Rae Kim 32 Amit Roy 33, 32 Xusi Han 32 Juan Esquivel-Rodríguez 34, 35 Daisuke Kihara 32, 35 Xiaofeng Yu 34 Neil J. Bruce 34 Jonathan C. Fuller 34 Rebbecca Wade 36, 34, 37 Ivan Anishchenko 38 Petras Kundrotas 38 Ilya Vakser 38, 39 Kenichiro Imai 39 Kazunori Yamada 39 Toshiyuki Oda 39 Tsukasa Nakamura 40 Kentaro Tomii 39, 40 Chiara Pallara 41 Miguel Romero-Durana 41 Brian Jiménez-García 41 Iain H Moal 42 Juan Fernández-Recio 42 Jong Young Joung 43 Jong Yun Kim 43 Keehyoung Joo 43, 44 Jooyoung Lee 43, 44 Dima Kozakov 45 Sandor Vajda 45, 46 Scott Mottarella 45 David Hall 45 Dmitri Beglov 45 Artem Mamonov 45 Bing Xia 45 Tanggis Bohnuud 45 Carlos del Carpio 47, 48 Eichiro Ichiishi 49 Nicholas Marze 50 Daisuke Kuroda 50 Shourya Burman 50 Jeffrey J Gray 51, 50 Edrisse Chermak 52 Luigi Cavallo 52 Romina Oliva 53 Andrey Tovchigrechko 54 Shoshana J Wodak 55
13 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
17 CAPSID - Computational Algorithms for Protein Structures and Interactions
Inria Nancy - Grand Est, LORIA - AIS - Department of Complex Systems, Artificial Intelligence & Robotics
25 AMIG - Assemblage moléculaire et intégrité du génome
B3S - Département Biochimie, Biophysique et Biologie Structurale
Abstract : We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. This article is protected by copyright. All rights reserved.
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Submitted on : Thursday, April 28, 2016 - 7:04:47 PM
Last modification on : Sunday, January 3, 2021 - 5:00:04 PM

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Marc F. Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen-You Huang, Dina Schneidman-Duhovy, et al.. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins - Structure, Function and Bioinformatics, Wiley, 2016, Special Issue: Eleventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, 84 (S1), pp.323-348. ⟨10.1002/prot.25007⟩. ⟨hal-01309105⟩



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