Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Marc F. Lensink*, Sameer Velankar, Andriy Kryshtafovych, Shen You Huang, Dina Schneidman-Duhovny, Andrej Sali, Joan Segura, Narcis Fernandez-Fuentes, Shruthi Viswanath, Ron Elber, Sergei Grudinin, Petr Popov, Emilie Neveu, Hasup Lee, Minkyung Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo QinHuan Xiang Zhou, David W. Ritchie, Bernard Maigret, Marie Dominique Devignes, Anisah Ghoorah, Mieczyslaw Torchala, Raphaël A.G. Chaleil, Paul A. Bates, Efrat Ben-Zeev, Miriam Eisenstein, Surendra S. Negi, Zhiping Weng, Thom Vreven, Brian G. Pierce, Tyler M. Borrman, Jinchao Yu, Françoise Ochsenbein, Raphaël Guerois, Anna Vangone, João P.G.L.M. Rodrigues, Gydo Van Zundert, Mehdi Nellen, Li Xue, Ezgi Karaca, Adrien S.J. Melquiond, Koen Visscher, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Shen, Lenna X. Peterson, Hyung Rae Kim, Amit Roy, Xusi Han, Juan Esquivel-Rodriguez, Daisuke Kihara, Xiaofeng Yu, Neil J. Bruce, Jonathan C. Fuller, Rebecca C. Wade, Ivan Anishchenko, Petras J. Kundrotas, Ilya A. Vakser, Kenichiro Imai, Kazunori Yamada, Toshiyuki Oda, Tsukasa Nakamura, Kentaro Tomii, Chiara Pallara, Miguel Romero-Durana, Brian Jiménez-García, Iain H. Moal, Juan Férnandez-Recio, Jong Young Joung, Jong Yun Kim, Keehyoung Joo, Jooyoung Lee, Dima Kozakov, Sandor Vajda, Scott Mottarella, David R. Hall, Dmitri Beglov, Artem Mamonov, Bing Xia, Tanggis Bohnuud, Carlos A. Del Carpio, Eichiro Ichiishi, Nicholas Marze, Daisuke Kuroda, Shourya S. Roy Burman, Jeffrey J. Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva, Andrey Tovchigrechko, Shoshana J. Wodak

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

119 Scopus citations


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.

Original languageAmerican English
Pages (from-to)323-348
Number of pages26
JournalProteins: Structure, Function and Bioinformatics
StatePublished - 2016
Externally publishedYes

Bibliographical note

Funding Information:
Additional Supporting Information may be found in the online version of this article. Grant sponsor: NIH; Grant numbers: R01 GM083960; P41 GM109824; GM058187; R01 GM061867; R01 GM093147; R01 GM078221; R01GM109980; R01GM094123; R01 GM097528; R01GM074255; Grant sponsor: Biotechnology and Biological Sciences Research Council; Grant number: BBS/E/W/10962A01D; Grant sponsor: Research Councils UK Academic Fellowship program; Grant sponsor: Cancer Research UK; Grant sponsor: Klaus Tschira Foundation; Grant sponsor: Platform Project for Supporting in Drug Discovery and Life Science Research; Grant sponsor: Japan Agency for Medical Research and Development; Grant sponsor: Agence Nationale de la Recherche; Grant number: ANR-11-MONU-0006; Grant sponsor: National Research Foundation of Korea (NRF); Grant numbers: NRF-2013R1A2A1A09012229; 2008-0061987; Grant sponsor: BIP; Grant number: ANR-IAB-2011-16-BIP:BIP; Grant sponsor: H2020 Marie Sklodowska-Curie Individual Fellowship; Grant number: 659025-BAP; Grant sponsor: Netherlands Organization for Scientific Research Veni; Grant number: 722.014.005; Grant sponsor: National Science Foundation; Grant numbers: CAREER Award DBI0953839; CCF- 1546278; NSF IIS1319551; NSF DBI1262189; NSF IOS1127027; NSF DBI1262621; NSF DBI 1458509; NSF AF 1527292; Grant sponsor: EU; Grant number: FP7 604102 (HBP); Grant sponsor: BMBF; Grant number: 0315749 (VLN); Grant sponsor: Spanish Ministry of Economy and Competitiveness; Grant number: BIO2013-48213-R; Grant sponsor: European Union; Grant number: FP7/2007- 2013 REA PIEF-GA-2012-327899; Grant sponsor: National Institute of Supercomputing and Networking; Grant number: KSC-2014-C3-01; Grant sponsor: USIsrael BSF; Grant number: 2009418; Grant sponsor: Regione Campania; Grant number: LR5-AF2008.

Publisher Copyright:
© 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.


  • Blind prediction
  • CASP
  • Oligomer state
  • Protein docking
  • Protein interaction


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