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

Handle URI:
http://hdl.handle.net/10754/621411
Title:
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
Authors:
Lensink, Marc F. ( 0000-0003-3957-9470 ) ; 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. ( 0000-0001-7369-1322 ) ; Xu, Xianjin; Qiu, Liming; Yan, Chengfei; Li, Jilong; Ma, Zhiwei; Cheng, Jianlin; Zou, Xiaoqin; Shen, Yang ( 0000-0003-4728-1973 ) ; 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. ( 0000-0001-6380-2324 ) ; Chermak, Edrisse ( 0000-0002-2716-5724 ) ; Cavallo, Luigi ( 0000-0002-1398-338X ) ; Oliva, Romina; Tovchigrechko, Andrey; Wodak, Shoshana J.
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.
KAUST Department:
King Abdullah University of Science and Technology; Saudi Arabia
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.
Publisher:
Wiley-Blackwell
Journal:
Proteins: Structure, Function, and Bioinformatics
Issue Date:
28-Apr-2016
DOI:
10.1002/prot.25007
Type:
Article
ISSN:
0887-3585
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]
Appears in Collections:
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dc.contributor.authorLensink, Marc F.en
dc.contributor.authorVelankar, Sameeren
dc.contributor.authorKryshtafovych, Andriyen
dc.contributor.authorHuang, Shen-Youen
dc.contributor.authorSchneidman-Duhovny, Dinaen
dc.contributor.authorSali, Andrejen
dc.contributor.authorSegura, Joanen
dc.contributor.authorFernandez-Fuentes, Narcisen
dc.contributor.authorViswanath, Shruthien
dc.contributor.authorElber, Ronen
dc.contributor.authorGrudinin, Sergeien
dc.contributor.authorPopov, Petren
dc.contributor.authorNeveu, Emilieen
dc.contributor.authorLee, Hasupen
dc.contributor.authorBaek, Minkyungen
dc.contributor.authorPark, Sangwooen
dc.contributor.authorHeo, Limen
dc.contributor.authorRie Lee, Gyuen
dc.contributor.authorSeok, Chaoken
dc.contributor.authorQin, Sanboen
dc.contributor.authorZhou, Huan-Xiangen
dc.contributor.authorRitchie, David W.en
dc.contributor.authorMaigret, Bernarden
dc.contributor.authorDevignes, Marie-Dominiqueen
dc.contributor.authorGhoorah, Anisahen
dc.contributor.authorTorchala, Mieczyslawen
dc.contributor.authorChaleil, Raphaël A.G.en
dc.contributor.authorBates, Paul A.en
dc.contributor.authorBen-Zeev, Efraten
dc.contributor.authorEisenstein, Miriamen
dc.contributor.authorNegi, Surendra S.en
dc.contributor.authorWeng, Zhipingen
dc.contributor.authorVreven, Thomen
dc.contributor.authorPierce, Brian G.en
dc.contributor.authorBorrman, Tyler M.en
dc.contributor.authorYu, Jinchaoen
dc.contributor.authorOchsenbein, Françoiseen
dc.contributor.authorGuerois, Raphaëlen
dc.contributor.authorVangone, Annaen
dc.contributor.authorRodrigues, João P.G.L.M.en
dc.contributor.authorvan Zundert, Gydoen
dc.contributor.authorNellen, Mehdien
dc.contributor.authorXue, Lien
dc.contributor.authorKaraca, Ezgien
dc.contributor.authorMelquiond, Adrien S.J.en
dc.contributor.authorVisscher, Koenen
dc.contributor.authorKastritis, Panagiotis L.en
dc.contributor.authorBonvin, Alexandre M.J.J.en
dc.contributor.authorXu, Xianjinen
dc.contributor.authorQiu, Limingen
dc.contributor.authorYan, Chengfeien
dc.contributor.authorLi, Jilongen
dc.contributor.authorMa, Zhiweien
dc.contributor.authorCheng, Jianlinen
dc.contributor.authorZou, Xiaoqinen
dc.contributor.authorShen, Yangen
dc.contributor.authorPeterson, Lenna X.en
dc.contributor.authorKim, Hyung-Raeen
dc.contributor.authorRoy, Amiten
dc.contributor.authorHan, Xusien
dc.contributor.authorEsquivel-Rodriguez, Juanen
dc.contributor.authorKihara, Daisukeen
dc.contributor.authorYu, Xiaofengen
dc.contributor.authorBruce, Neil J.en
dc.contributor.authorFuller, Jonathan C.en
dc.contributor.authorWade, Rebecca C.en
dc.contributor.authorAnishchenko, Ivanen
dc.contributor.authorKundrotas, Petras J.en
dc.contributor.authorVakser, Ilya A.en
dc.contributor.authorImai, Kenichiroen
dc.contributor.authorYamada, Kazunorien
dc.contributor.authorOda, Toshiyukien
dc.contributor.authorNakamura, Tsukasaen
dc.contributor.authorTomii, Kentaroen
dc.contributor.authorPallara, Chiaraen
dc.contributor.authorRomero-Durana, Miguelen
dc.contributor.authorJiménez-García, Brianen
dc.contributor.authorMoal, Iain H.en
dc.contributor.authorFérnandez-Recio, Juanen
dc.contributor.authorJoung, Jong Youngen
dc.contributor.authorKim, Jong Yunen
dc.contributor.authorJoo, Keehyoungen
dc.contributor.authorLee, Jooyoungen
dc.contributor.authorKozakov, Dimaen
dc.contributor.authorVajda, Sandoren
dc.contributor.authorMottarella, Scotten
dc.contributor.authorHall, David R.en
dc.contributor.authorBeglov, Dmitrien
dc.contributor.authorMamonov, Artemen
dc.contributor.authorXia, Bingen
dc.contributor.authorBohnuud, Tanggisen
dc.contributor.authorDel Carpio, Carlos A.en
dc.contributor.authorIchiishi, Eichiroen
dc.contributor.authorMarze, Nicholasen
dc.contributor.authorKuroda, Daisukeen
dc.contributor.authorRoy Burman, Shourya S.en
dc.contributor.authorGray, Jeffrey J.en
dc.contributor.authorChermak, Edrisseen
dc.contributor.authorCavallo, Luigien
dc.contributor.authorOliva, Rominaen
dc.contributor.authorTovchigrechko, Andreyen
dc.contributor.authorWodak, Shoshana J.en
dc.date.accessioned2016-11-03T08:28:40Z-
dc.date.available2016-11-03T08:28:40Z-
dc.date.issued2016-04-28en
dc.identifier.citationLensink 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.en
dc.identifier.issn0887-3585en
dc.identifier.doi10.1002/prot.25007en
dc.identifier.urihttp://hdl.handle.net/10754/621411-
dc.description.abstractWe 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.en
dc.description.sponsorshipRegione Campania[LR5-AF2008]en
dc.description.sponsorshipNational Science Foundation[CAREER Award DBI0953839, NSF IIS1319551, NSF DBI1262621, NSF DBI 1458509, CCF-1546278, NSF IOS1127027, NSF AF 1527292, NSF DBI1262189]en
dc.description.sponsorshipNational Research Foundation of Korea[2008-0061987, NRF-2013R1A2A1A09012229]en
dc.description.sponsorshipAgence Nationale de la Recherche[ANR-11-MONU-0006]en
dc.description.sponsorshipJapan Agency for Medical Research and Developmenten
dc.description.sponsorshipKlaus Tschira Stiftungen
dc.description.sponsorshipCancer Research UKen
dc.description.sponsorshipBiotechnology and Biological Sciences Research Council[BBS/E/W/10962A01D]en
dc.description.sponsorshipNIH[R01GM074255, R01GM094123, R01GM109980, R01 GM078221, R01 GM097528, R01 GM093147, P41 GM109824, R01 GM061867, R01 GM083960, GM058187]en
dc.description.sponsorshipResearch Councils UK Academic Fellowship programen
dc.description.sponsorshipPlatform Project for Supporting in Drug Discovery and Life Science Researchen
dc.description.sponsorshipBIP[ANR-IAB-2011-16-BIP:BIP]en
dc.description.sponsorshipH2020 Marie Sklodowska-Curie Individual Fellowship[659025-BAP]en
dc.description.sponsorshipNetherlands Organization for Scientific Research Veni[722.014.005]en
dc.description.sponsorshipEU[FP7 604102 (HBP)]en
dc.description.sponsorshipBMBF[0315749 (VLN)]en
dc.description.sponsorshipSpanish Ministry of Economy and Competitiveness[BIO2013-48213-R]en
dc.description.sponsorshipEuropean Union[FP7/2007-2013 REA PIEF-GA-2012-327899]en
dc.description.sponsorshipNational Institute of Supercomputing and Networking[KSC-2014-C3-01]en
dc.description.sponsorshipUS-Israel BSF[2009418]en
dc.publisherWiley-Blackwellen
dc.subjectBlind predictionen
dc.titlePrediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experimenten
dc.typeArticleen
dc.contributor.departmentKing Abdullah University of Science and Technology; Saudi Arabiaen
dc.identifier.journalProteins: Structure, Function, and Bioinformaticsen
dc.contributor.institutionUniversity Lille; CNRS UMR8576 UGSF Lille F-59000 Franceen
dc.contributor.institutionEuropean Molecular Biology Laboratory; European Bioinformatics Institute (EMBL-EBI); Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdomen
dc.contributor.institutionGenome Center; University of California; Davis California 95616en
dc.contributor.institutionResearch Support Computing, University of Missouri Bioinformatics Consortium, and Department of Computer Science, University of Missouri; Columbia Missouri 65211en
dc.contributor.institutionDepartment of Bioengineering and Therapeutic Sciences; University of California San Francisco; San Francisco California 94158en
dc.contributor.institutionDepartment of Pharmaceutical Chemistry; University of California San Francisco; San Francisco California 94158en
dc.contributor.institutionCalifornia Institute for Quantitative Biosciences (QB3); University of California San Francisco; San Francisco California 94158en
dc.contributor.institutionGN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC); Madrid 28049 Spainen
dc.contributor.institutionInstitute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University; Aberystwyth SY233FG United Kingdomen
dc.contributor.institutionDepartment of Computer Science; University of Texas at Austin; Austin Texas 78712en
dc.contributor.institutionInstitute for Computational Engineering and Sciences, University of Texas at Austin; Austin Texas 78712en
dc.contributor.institutionDepartment of Chemistry; University of Texas at Austin; Austin Texas 78712en
dc.contributor.institutionLJK, University Grenoble Alpes, CNRS; Grenoble 38000 Franceen
dc.contributor.institutionINRIA; Grenoble 38000 Franceen
dc.contributor.institutionMoscow Institute of Physics and Technology; Dolgoprudniy Russiaen
dc.contributor.institutionDepartment of Chemistry; Seoul National University; Seoul 151-747 Republic of Koreaen
dc.contributor.institutionDepartment of Physics and Institute of Molecular Biophysics; Florida State University; Tallahassee Florida 32306 USAen
dc.contributor.institutionINRIA Nancy-Grand Est; Villers-lès-Nancy 54600 Franceen
dc.contributor.institutionCNRS, LORIA; Campus Scientifique, BP 239 Vandœuvre-lès-Nancy 54506 Franceen
dc.contributor.institutionDepartment of Computer Science and Engineering; University of Mauritius; Reduit Mauritiusen
dc.contributor.institutionBiomolecular Modelling Laboratory, the Francis Crick Institute, Lincoln's Inn Fields Laboratory; London WC2A 3LY United Kingdomen
dc.contributor.institutionG-INCPM, Weizmann Institute of Science; Rehovot 7610001 Israelen
dc.contributor.institutionDepartment of Chemical Research Support; Weizmann Institute of Science; Rehovot 7610001 Israelen
dc.contributor.institutionSealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch; 301 University Boulevard Galveston Texas 77555-0857en
dc.contributor.institutionProgram in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Worcester Massachusetts 01605en
dc.contributor.institutionInstitute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Saclay, CEA-Saclay; Gif-sur-Yvette 91191 Franceen
dc.contributor.institutionBijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University; Padualaan 8 Utrecht 3584 CH The Netherlandsen
dc.contributor.institutionDalton Cardiovascular Research Center, University of Missouri; Columbia Missouri 65211en
dc.contributor.institutionDepartment of Physics and Astronomy; University of Missouri; Columbia Missouri 65211en
dc.contributor.institutionDepartment of Computer Science; University of Missouri; Columbia Missouri 65211en
dc.contributor.institutionInformatics Institute, University of Missouri; Columbia Missouri 65211en
dc.contributor.institutionDepartment of Biochemistry; University of Missouri; Columbia Missouri 65211en
dc.contributor.institutionToyota Technological Institute at Chicago; 6045 S Kenwood Avenue Chicago Illinois 60637en
dc.contributor.institutionDepartment of Biological Sciences; Purdue University; West Lafayette Indiana 47907en
dc.contributor.institutionBioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institutes of Health; Hamilton Montano 59840en
dc.contributor.institutionDepartment of Computer Science; Purdue University; West Lafayette IN USA 47907en
dc.contributor.institutionMolecular and Cellular Modeling Group; Heidelberg Institute for Theoretical Studies (HITS); Heidelberg Germanyen
dc.contributor.institutionCenter for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University; Heidelberg Germanyen
dc.contributor.institutionInterdisciplinary Center for Scientific Computing (IWR), Heidelberg University; Heidelberg Germanyen
dc.contributor.institutionCenter for Computational Biology, The University of Kansas; Lawrence Kansas 66047en
dc.contributor.institutionDepartment of Molecular Biosciences; The University of Kansas; Lawrence Kansas 66047en
dc.contributor.institutionComputational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST); Koto-Ku Japanen
dc.contributor.institutionGraduate School of Frontier Sciences; the University of Tokyo; Kashiwa Japanen
dc.contributor.institutionJoint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center; C/Jordi Girona 29 Barcelona 08034 Spainen
dc.contributor.institutionCenter for in-Silico Protein Science, Korea Institute for Advanced Study; Seoul 130-722 Koreaen
dc.contributor.institutionCenter for Advanced Computation, Korea Institute for Advanced Study; Seoul 130-722 Koreaen
dc.contributor.institutionSchool of Computational Science; Korea Institute for Advanced Study; Seoul 130-722 Koreaen
dc.contributor.institutionDepartment of Biomedical Engineering; Boston University; Boston Massachusettsen
dc.contributor.institutionDepartment of Chemistry; Boston University; Boston Massachusettsen
dc.contributor.institutionInstitute of Biological Diversity, International Pacific Institute of Indiana; Bloomington Indiana 47401en
dc.contributor.institutionDrosophila Genetic Resource Center, Kyoto Institute of Technology; Ukyo-Ku 616-8354 Japanen
dc.contributor.institutionInternational University of Health and Welfare Hospital (IUHW Hospital); Asushiobara-City, Tochigi Prefecture 329-2763 Japanen
dc.contributor.institutionDepartment of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore Maryland 21218en
dc.contributor.institutionProgram in Molecular Biophysics, Johns Hopkins University; Baltimore Maryland 21218en
dc.contributor.institutionUniversity of Naples “Parthenope”; Napoli Italyen
dc.contributor.institutionJ. Craig Venter Institute; 9704 Medical Center Drive Rockville Maryland 20850en
dc.contributor.institutionDepartments of Biochemistry and Molecular Genetics; University of Toronto; Toronto Ontario Canadaen
dc.contributor.institutionVIB Structural Biology Research Center; VUB Pleinlaan 2 Brussels 1050 Belgiumen
kaust.authorChermak, Edrisseen
kaust.authorCavallo, Luigien
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