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 Zhiping Weng 23 Raphaël Guerois 24 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 25 Liming Qiu 25 Chengfei Yan 26, 25 Jilong Li 27 Zhiwei Ma 25, 26 Jianlin Cheng 27, 28 Xiaoqin Zou 25, 26, 28, 29 Yang Sheng 30 Lenna Peterson 31 Hyung-Rae Kim 31 Amit Roy 32, 31 Xusi Han 31 Juan Esquivel-Rodríguez 33, 34 Daisuke Kihara 31, 34 Xiaofeng Yu 33 Neil J. Bruce 33 Jonathan C. Fuller 33 Rebbecca Wade 35, 33, 36 Ivan Anishchenko 37 Petras Kundrotas 37 Ilya Vakser 37, 38 Kenichiro Imai 38 Kazunori Yamada 38 Toshiyuki Oda 38 Tsukasa Nakamura 39 Kentaro Tomii 38, 39 Chiara Pallara 40 Miguel Romero-Durana 40 Brian Jiménez-García 40 Iain H Moal 41 Juan Fernández-Recio 41 Jong Young Joung 42 Jong Yun Kim 42 Keehyoung Joo 42, 43 Jooyoung Lee 42, 43 Dima Kozakov 44 Sandor Vajda 44, 45 Scott Mottarella 44 David Hall 44 Dmitri Beglov 44 Artem Mamonov 44 Bing Xia 44 Tanggis Bohnuud 44 Carlos del Carpio 46, 47 Eichiro Ichiishi 48 Nicholas Marze 49 Daisuke Kuroda 49 Shourya Burman 49 Jeffrey J Gray 50, 49 Edrisse Chermak 51 Luigi Cavallo 51 Romina Oliva 52 Andrey Tovchigrechko 53 Shoshana J Wodak 54
13 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
17 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.
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Submitted on : Thursday, April 28, 2016 - 7:04:47 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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