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Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling

Title: Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Name(s): Lensink, Marc F, author
Velankar, Sameer, author
Kryshtafovych, Andriy, author
Huang, Shen-You, author
Schneidman-Duhovny, Dina, author
Sali, Andrej, author
Segura, Joan, author
Fernandez-Fuentes, Narcis, author
Viswanath, Shruthi, author
Elber, Ron, author
Grudinin, Sergei, author
Popov, Petr, author
Neveu, Emilie, author
Lee, Hasup, author
Baek, Minkyung, author
Park, Sangwoo, author
Heo, Lim, author
Rie Lee, Gyu, author
Seok, Chaok, author
Qin, Sanbo, author
Zhou, Huan-Xiang, author
Ritchie, David W, author
Maigret, Bernard, author
Devignes, Marie-Dominique, author
Ghoorah, Anisah, author
Torchala, Mieczyslaw, author
Chaleil, Raphaël A G, author
Bates, Paul A, author
Ben-Zeev, Efrat, author
Eisenstein, Miriam, author
Negi, Surendra S, author
Weng, Zhiping, author
Vreven, Thom, author
Pierce, Brian G, author
Borrman, Tyler M, author
Yu, Jinchao, author
Ochsenbein, Françoise, author
Guerois, Raphaël, author
Vangone, Anna, author
Rodrigues, João P G L M, author
van Zundert, Gydo, author
Nellen, Mehdi, author
Xue, Li, author
Karaca, Ezgi, author
Melquiond, Adrien S J, author
Visscher, Koen, author
Kastritis, Panagiotis L, author
Bonvin, Alexandre M J J, author
Xu, Xianjin, author
Qiu, Liming, author
Yan, Chengfei, author
Li, Jilong, author
Ma, Zhiwei, author
Cheng, Jianlin, author
Zou, Xiaoqin, author
Shen, Yang, author
Peterson, Lenna X, author
Kim, Hyung-Rae, author
Roy, Amit, author
Han, Xusi, author
Esquivel-Rodriguez, Juan, author
Kihara, Daisuke, author
Yu, Xiaofeng, author
Bruce, Neil J, author
Fuller, Jonathan C, author
Wade, Rebecca C, author
Anishchenko, Ivan, author
Kundrotas, Petras J, author
Vakser, Ilya A, author
Imai, Kenichiro, author
Yamada, Kazunori, author
Oda, Toshiyuki, author
Nakamura, Tsukasa, author
Tomii, Kentaro, author
Pallara, Chiara, author
Romero-Durana, Miguel, author
Jiménez-García, Brian, author
Moal, Iain H, author
Férnandez-Recio, Juan, author
Joung, Jong Young, author
Kim, Jong Yun, author
Joo, Keehyoung, author
Lee, Jooyoung, author
Kozakov, Dima, author
Vajda, Sandor, author
Mottarella, Scott, author
Hall, David R, author
Beglov, Dmitri, author
Mamonov, Artem, author
Xia, Bing, author
Bohnuud, Tanggis, author
Del Carpio, Carlos A, author
Ichiishi, Eichiro, author
Marze, Nicholas, author
Kuroda, Daisuke, author
Roy Burman, Shourya S, author
Gray, Jeffrey J, author
Chermak, Edrisse, author
Cavallo, Luigi, author
Oliva, Romina, author
Tovchigrechko, Andrey, author
Wodak, Shoshana J, author
Type of Resource: text
Genre: Journal Article
Date Issued: 2016-09-01
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: 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. Proteins 2016; 84(Suppl 1):323-348. © 2016 Wiley Periodicals, Inc.
Identifier: FSU_pmch_27122118 (IID), 10.1002/prot.25007 (DOI), PMC5030136 (PMCID), 27122118 (RID), 27122118 (EID)
Keywords: CAPRI, CASP, Blind prediction, Oligomer state, Protein docking, Protein interaction
Grant Number: R01 GM074255, R01 GM109980, R01 GM078221, R01 GM100482, R01 GM058187, R01 GM093123, R01 GM083960, P41 GM109824, R01 GM061867, R01 GM093147, R01 GM097528, BBS/E/W/10962A01D,
Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at
Subject(s): Algorithms
Amino Acid Motifs
Binding Sites
Computational Biology/methods
Computational Biology/statistics & numerical data
International Cooperation
Models, Statistical
Molecular Docking Simulation
Molecular Dynamics Simulation
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Folding
Protein Interaction Domains and Motifs
Protein Multimerization
Protein Structure, Tertiary
Sequence Homology, Amino Acid
Persistent Link to This Record:
Host Institution: FSU
Is Part Of: Proteins.
Issue: vol. 84 Suppl 1

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Lensink, M. F., Velankar, S., Kryshtafovych, A., Huang, S. -Y., Schneidman-Duhovny, D., Sali, A., … Wodak, S. J. (2016). Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins. Retrieved from