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

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...

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Vydané v:	Proteins, structure, function, and bioinformatics Ročník 84; číslo S1; s. 323 - 348
Hlavní autori:	Lensink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, 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, Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, Wodak, Shoshana J.
Médium:	Journal Article Publikácia
Jazyk:	English
Vydavateľské údaje:	United States Blackwell Publishing Ltd 01.09.2016 Wiley Subscription Services, Inc Wiley John Wiley and Sons Inc
Predmet:	Algorithms Amino Acid Motifs Bacteria - chemistry Binding Sites Bioinformatics blind prediction CAPRI CAPRI Round 30 CASP Computational Biology - methods Computational Biology - statistics & numerical data Enginyeria biomèdica Heteroprotein Homoprotein Humans International Cooperation Internet Investigació Models, Statistical Molecular Docking Simulation Molecular Dynamics Simulation oligomer state Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand protein docking Protein Folding protein interaction Protein Interaction Domains and Motifs Protein Multimerization Protein Structure, Tertiary Protein-protein docking Proteins Proteins - chemistry Proteïnes Sequence Homology, Amino Acid Software Thermodynamics Àrees temàtiques de la UPC protein interaction CASP blind prediction protein docking CAPRI oligomer state
ISSN:	0887-3585, 1097-0134, 1097-0134
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Shrnutí:	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. Proteins 2016; 84(Suppl 1):323–348. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Bibliografia:	European Union - No. FP7/2007-2013 REA PIEF-GA-2012-327899 US-Israel BSF - No. 2009418 Regione Campania - No. LR5-AF2008 Cancer Research UK National Research Foundation of Korea (NRF) - No. NRF-2013R1A2A1A09012229; No. 2008-0061987 EU - No. FP7 604102 (HBP) Netherlands Organization for Scientific Research Veni - No. 722.014.005 Biotechnology and Biological Sciences Research Council - No. BBS/E/W/10962A01D ArticleID:PROT25007 National Institute of Supercomputing and Networking - No. KSC-2014-C3-01 Spanish Ministry of Economy and Competitiveness - No. BIO2013-48213-R H2020 Marie Sklodowska-Curie Individual Fellowship - No. 659025-BAP Klaus Tschira Foundation Research Councils UK Academic Fellowship program National Science Foundation - No. CAREER Award DBI0953839; No. CCF-1546278; No. NSF IIS1319551; No. NSF DBI1262189; No. NSF IOS1127027; No. NSF DBI1262621; No. NSF DBI 1458509; No. NSF AF 1527292 ark:/67375/WNG-Q5S5D80D-X BIP - No. ANR-IAB-2011-16-BIP:BIP Japan Agency for Medical Research and Development NIH - No. R01 GM083960; No. P41 GM109824; No. GM058187; No. R01 GM061867; No. R01 GM093147; No. R01 GM078221; No. R01GM109980; No. R01GM094123; No. R01 GM097528; No. R01GM074255 Agence Nationale de la Recherche - No. ANR-11-MONU-0006 istex:F23E83CFCD6766C0C8C420640F64605D34D9BFE6 Platform Project for Supporting in Drug Discovery and Life Science Research BMBF - No. 0315749 (VLN) The copyright line for this article was changed on 6 October 2016 after original online publication. ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	0887-3585 1097-0134 1097-0134
DOI:	10.1002/prot.25007