Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
Type
ArticleAuthors
Lensink, Marc F.
Velankar, Sameer
Kryshtafovych, Andriy

Huang, Shen-You
Schneidman-Duhovny, Dina
Sali, Andrej
Segura, Joan
Fernandez-Fuentes, Narcis
Viswanath, Shruthi
Elber, Ron
Grudinin, Sergei
Popov, Petr
Neveu, Emilie
Lee, Hasup
Baek, Minkyung
Park, Sangwoo
Heo, Lim
Rie Lee, Gyu
Seok, Chaok
Qin, Sanbo
Zhou, Huan-Xiang
Ritchie, David W.
Maigret, Bernard
Devignes, Marie-Dominique
Ghoorah, Anisah
Torchala, Mieczyslaw
Chaleil, Raphaël A.G.
Bates, Paul A.
Ben-Zeev, Efrat
Eisenstein, Miriam
Negi, Surendra S.
Weng, Zhiping
Vreven, Thom
Pierce, Brian G.
Borrman, Tyler M.
Yu, Jinchao
Ochsenbein, Françoise
Guerois, Raphaël
Vangone, Anna
Rodrigues, João P.G.L.M.
van Zundert, Gydo
Nellen, Mehdi
Xue, Li
Karaca, Ezgi
Melquiond, Adrien S.J.
Visscher, Koen
Kastritis, Panagiotis L.
Bonvin, Alexandre M.J.J.

Xu, Xianjin
Qiu, Liming
Yan, Chengfei
Li, Jilong
Ma, Zhiwei
Cheng, Jianlin
Zou, Xiaoqin
Shen, Yang

Peterson, Lenna X.
Kim, Hyung-Rae
Roy, Amit
Han, Xusi
Esquivel-Rodriguez, Juan
Kihara, Daisuke
Yu, Xiaofeng
Bruce, Neil J.
Fuller, Jonathan C.
Wade, Rebecca C.
Anishchenko, Ivan
Kundrotas, Petras J.
Vakser, Ilya A.
Imai, Kenichiro
Yamada, Kazunori
Oda, Toshiyuki
Nakamura, Tsukasa
Tomii, Kentaro
Pallara, Chiara
Romero-Durana, Miguel
Jiménez-García, Brian
Moal, Iain H.
Férnandez-Recio, Juan
Joung, Jong Young
Kim, Jong Yun
Joo, Keehyoung
Lee, Jooyoung
Kozakov, Dima
Vajda, Sandor
Mottarella, Scott
Hall, David R.
Beglov, Dmitri
Mamonov, Artem
Xia, Bing
Bohnuud, Tanggis
Del Carpio, Carlos A.
Ichiishi, Eichiro
Marze, Nicholas
Kuroda, Daisuke
Roy Burman, Shourya S.
Gray, Jeffrey J.

Chermak, Edrisse

Cavallo, Luigi

Oliva, Romina

Tovchigrechko, Andrey
Wodak, Shoshana J.
KAUST Department
Chemical Science ProgramKAUST Catalysis Center (KCC)
Physical Science and Engineering (PSE) Division
Date
2016-04-28Online Publication Date
2016-06-01Print Publication Date
2016-09Embargo End Date
2017-04-28Permanent link to this record
http://hdl.handle.net/10754/621411
Metadata
Show full item recordAbstract
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. © 2016 Wiley Periodicals, Inc.Citation
Lensink MF, Velankar S, Kryshtafovych A, Huang S-Y, Schneidman-Duhovny D, et al. (2016) Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins: Structure, Function, and Bioinformatics 84: 323–348. Available: http://dx.doi.org/10.1002/prot.25007.Sponsors
Regione Campania[LR5-AF2008]National Science Foundation[CAREER Award DBI0953839, NSF IIS1319551, NSF DBI1262621, NSF DBI 1458509, CCF-1546278, NSF IOS1127027, NSF AF 1527292, NSF DBI1262189]
National Research Foundation of Korea[2008-0061987, NRF-2013R1A2A1A09012229]
Agence Nationale de la Recherche[ANR-11-MONU-0006]
Japan Agency for Medical Research and Development
Klaus Tschira Stiftung
Cancer Research UK
Biotechnology and Biological Sciences Research Council[BBS/E/W/10962A01D]
NIH[R01GM074255, R01GM094123, R01GM109980, R01 GM078221, R01 GM097528, R01 GM093147, P41 GM109824, R01 GM061867, R01 GM083960, GM058187]
Research Councils UK Academic Fellowship program
Platform Project for Supporting in Drug Discovery and Life Science Research
BIP[ANR-IAB-2011-16-BIP:BIP]
H2020 Marie Sklodowska-Curie Individual Fellowship[659025-BAP]
Netherlands Organization for Scientific Research Veni[722.014.005]
EU[FP7 604102 (HBP)]
BMBF[0315749 (VLN)]
Spanish Ministry of Economy and Competitiveness[BIO2013-48213-R]
European Union[FP7/2007-2013 REA PIEF-GA-2012-327899]
National Institute of Supercomputing and Networking[KSC-2014-C3-01]
US-Israel BSF[2009418]
Publisher
WileyPubMed ID
27122118Additional Links
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030136https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030136
ae974a485f413a2113503eed53cd6c53
10.1002/prot.25007
Scopus Count
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