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

Marc F. Lensink 1, 2 Sameer Velankar 3, 2 Andriy Kryshtafovych 4, 2 Shen-You Huang 5, 6, 2 Dina Schneidman-Duhovy 7, 8, 2 Andrej Sali 9, 2 Joan Segura 10, 2 Narcis Fernandez-Fuentes 11, 2 Shruthi Viswanath 12, 13, 2 Ron Elber 12, 14, 2 Sergei Grudinin 15 Petr Popov 16, 15 Emilie Neveu 15 Hasup Lee 17, 2 Minkyung Baek 17, 2 Sangwoo Park 17, 2 Lim Heo 17, 2 Gyu Rie Lee 17, 2 Chaok Seok 17, 2 Sanbo Qin 18, 2 Huan-Xiang Zhou 18, 2 David W. Ritchie 19, 2 Bernard Maigret 19, 2 Marie-Dominique Devignes 19, 2 Anisah Ghoorah 20, 2 Mieczyslaw Torchala 21, 2 Raphaël Chaleil 21, 2 Paul A Bates 21, 2 Efrat Ben-Zeev 22, 2 Miriam Eisenstein 23, 2 Surendra Negi S. 24, 2 Thom Vreven 25, 2 Brian G Pierce 25, 2 Tyler Borrman 25, 2 Jinchao Yu 25, 2 Francoise Ochsenbein 25, 2 Zhiping Weng 25, 2 Raphaël Guerois 25, 2 Anna Vangone 26, 2 João Rodrigues 26, 2 Gydo Van Zundert 26, 2 Mehdi Nellen 26, 2 Li Xue 26, 2 Ezgi Karaca 26, 2 Adrien S. J. Melquiond 26, 2 Koen Visscher 26, 2 Panagiotis L Kastritis 26, 2 Alexandre Bonvin 26, 2 Xianjin Xu 27, 2 Liming Qiu 27, 2 Chengfei Yan 28, 27, 2 Jilong Li 29, 2 Zhiwei Ma 27, 28, 2 Jianlin Cheng 29, 30, 2 Xiaoqin Zou 27, 28, 30, 31, 2 Yang Sheng 32, 2 Lenna Peterson 33, 2 Hyung-Rae Kim 33, 2 Amit Roy 34, 33, 2 Xusi Han 33, 2 Juan Esquivel-Rodríguez 35, 36, 2 Daisuke Kihara 33, 36, 2 Xiaofeng Yu 35, 2 Neil J. Bruce 35, 2 Jonathan C. Fuller 35, 2 Rebbecca Wade 37, 35, 38, 2 Ivan Anishchenko 39, 2 Petras Kundrotas 39, 2 Ilya Vakser 39, 40, 2 Kenichiro Imai 40, 2 Kazunori Yamada 40, 2 Toshiyuki Oda 40, 2 Tsukasa Nakamura 41, 2 Kentaro Tomii 40, 41, 2 Chiara Pallara 42, 2 Miguel Romero-Durana 42, 2 Brian Jiménez-García 42, 2 Iain H Moal 43, 2 Juan Fernández-Recio 43, 2 Jong Young Joung 44, 2 Jong Yun Kim 44, 2 Keehyoung Joo 44, 45, 2 Jooyoung Lee 44, 45, 2 Dima Kozakov 46, 2 Sandor Vajda 46, 47, 2 Scott Mottarella 46, 2 David Hall 46, 2 Dmitri Beglov 46, 2 Artem Mamonov 46, 2 Bing Xia 46, 2 Tanggis Bohnuud 46, 2 Carlos Del Carpio 48, 49, 2 Eichiro Ichiishi 50, 2 Nicholas Marze 51, 2 Daisuke Kuroda 51, 2 Shourya Burman 51, 2 Jeffrey J Gray 52, 51, 2 Edrisse Chermak 53, 2 Luigi Cavallo 53, 2 Romina Oliva 54, 2 Andrey Tovchigrechko 55, 2 Shoshana J Wodak 56, 2
15 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
19 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 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.
Type de document :
Article dans une revue
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〉
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Soumis le : jeudi 28 avril 2016 - 19:04:47
Dernière modification le : mardi 16 janvier 2018 - 17:06:01

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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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