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 8 Joan Segura 9 Narcis Fernandez-Fuentes 10 Shruthi Viswanath 11, 12 Ron Elber 11, 13 Sergei Grudinin 14 Petr Popov 15, 14 Emilie Neveu 14 Hasup Lee 16 Minkyung Baek 16 Sangwoo Park 16 Lim Heo 16 Gyu Rie Lee 16 Chaok Seok 16 Sanbo Qin 17 Huan-Xiang Zhou 17 David W. Ritchie 18 Bernard Maigret 18 Marie-Dominique Devignes 18 Anisah Ghoorah 19 Mieczyslaw Torchala 20 Raphaël Chaleil 20 Paul A Bates 20 Efrat Ben-Zeev 21 Miriam Eisenstein 22 Surendra Negi S. 23 Thom Vreven 24 Brian G Pierce 24 Tyler Borrman 24 Jinchao Yu 24 Francoise Ochsenbein 24 Zhiping Weng 24 Raphaël Guerois 24 Anna Vangone 25 João Rodrigues 25 Gydo Van Zundert 25 Mehdi Nellen 25 Li Xue 25 Ezgi Karaca 25 Adrien S. J. Melquiond 25 Koen Visscher 25 Panagiotis L Kastritis 25 Alexandre Bonvin 25 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
14 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
18 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〉
Liste complète des métadonnées

https://hal.inria.fr/hal-01309105
Contributeur : Nano-D Equipe <>
Soumis le : jeudi 28 avril 2016 - 19:04:47
Dernière modification le : vendredi 8 juin 2018 - 08:51:59

Lien texte intégral

Identifiants

Citation

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〉

Partager

Métriques

Consultations de la notice

1014