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

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    Authors
    Lensink, Marc F. cc
    Velankar, Sameer
    Kryshtafovych, Andriy cc
    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. cc
    Xu, Xianjin
    Qiu, Liming
    Yan, Chengfei
    Li, Jilong
    Ma, Zhiwei
    Cheng, Jianlin
    Zou, Xiaoqin
    Shen, Yang cc
    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. cc
    Chermak, Edrisse cc
    Cavallo, Luigi cc
    Oliva, Romina cc
    Tovchigrechko, Andrey
    Wodak, Shoshana J.
    KAUST Department
    Chemical Science Program
    KAUST Catalysis Center (KCC)
    Physical Science and Engineering (PSE) Division
    Date
    2016-04-28
    Online Publication Date
    2016-06-01
    Print Publication Date
    2016-09
    Embargo End Date
    2017-04-28
    Permanent link to this record
    http://hdl.handle.net/10754/621411
    
    Metadata
    Show full item record
    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. © 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
    Wiley
    Journal
    Proteins: Structure, Function, and Bioinformatics
    DOI
    10.1002/prot.25007
    PubMed ID
    27122118
    Additional Links
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030136
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030136
    ae974a485f413a2113503eed53cd6c53
    10.1002/prot.25007
    Scopus Count
    Collections
    Articles; Physical Science and Engineering (PSE) Division; Chemical Science Program; KAUST Catalysis Center (KCC)

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