Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
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. Th...
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2016 |
| País: | España |
| Institución: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/96562 |
| Acceso en línea: | https://hdl.handle.net/2117/96562 https://dx.doi.org/10.1002/prot.25007 |
| Access Level: | acceso abierto |
| Palabra clave: | Proteins Protein binding CAPRI Round 30 Homoprotein Heteroprotein Protein-protein docking Proteïnes--Investigació Àrees temàtiques de la UPC::Enginyeria biomèdica |
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| dc.title.none.fl_str_mv |
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment |
| title |
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment |
| spellingShingle |
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment Lesink, Marc F. Proteins Protein binding CAPRI Round 30 Homoprotein Heteroprotein Protein-protein docking Proteïnes--Investigació Àrees temàtiques de la UPC::Enginyeria biomèdica |
| title_short |
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment |
| title_full |
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment |
| title_fullStr |
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment |
| title_full_unstemmed |
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment |
| title_sort |
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment |
| dc.creator.none.fl_str_mv |
Lesink, Marc F. Velankar, Sameer Kryshtafovych, Andriy Huang, Shen-You Schneidman-Duhovny, Dina Sali, Andrej Segura, Joan Fernandez-Fuentes, Narcis Shruthi, Viswanath Elber, Ron Grudinin, Sergei Popov, Petr Neveu, Emilie Lee, Hasup Baek, Minkyung Park, Sangwoo Heo, Lim Lee, Gyu R. 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, Joao P.G.L.M. Zundert, Gydo van Nellen, Mehdi Xue, Li Karaca, Ezgi Melquiond, Adrien S.J. Visscher, Koen Kastritis, Panagiotis L. Bonvin, Alexandre M.J.J. Xianjin, Xu 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. Fernández-Recio, Juan Joung, Jong Y. Kim, Jong Y. 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 Burman, Shourya S. Gray, Jeffrey J. Chermak, Edrisse Cavallo, Luigi Oliva, Romina Tovchigrechko, Andrey Wodak, Shoshana J. |
| author |
Lesink, Marc F. |
| author_facet |
Lesink, Marc F. Velankar, Sameer Kryshtafovych, Andriy Huang, Shen-You Schneidman-Duhovny, Dina Sali, Andrej Segura, Joan Fernandez-Fuentes, Narcis Shruthi, Viswanath Elber, Ron Grudinin, Sergei Popov, Petr Neveu, Emilie Lee, Hasup Baek, Minkyung Park, Sangwoo Heo, Lim Lee, Gyu R. 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, Joao P.G.L.M. Zundert, Gydo van Nellen, Mehdi Xue, Li Karaca, Ezgi Melquiond, Adrien S.J. Visscher, Koen Kastritis, Panagiotis L. Bonvin, Alexandre M.J.J. Xianjin, Xu 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. Fernández-Recio, Juan Joung, Jong Y. Kim, Jong Y. 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 Burman, Shourya S. Gray, Jeffrey J. Chermak, Edrisse Cavallo, Luigi Oliva, Romina Tovchigrechko, Andrey Wodak, Shoshana J. |
| author_role |
author |
| author2 |
Velankar, Sameer Kryshtafovych, Andriy Huang, Shen-You Schneidman-Duhovny, Dina Sali, Andrej Segura, Joan Fernandez-Fuentes, Narcis Shruthi, Viswanath Elber, Ron Grudinin, Sergei Popov, Petr Neveu, Emilie Lee, Hasup Baek, Minkyung Park, Sangwoo Heo, Lim Lee, Gyu R. 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, Joao P.G.L.M. Zundert, Gydo van Nellen, Mehdi Xue, Li Karaca, Ezgi Melquiond, Adrien S.J. Visscher, Koen Kastritis, Panagiotis L. Bonvin, Alexandre M.J.J. Xianjin, Xu 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. Fernández-Recio, Juan Joung, Jong Y. Kim, Jong Y. 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 Burman, Shourya S. Gray, Jeffrey J. Chermak, Edrisse Cavallo, Luigi Oliva, Romina Tovchigrechko, Andrey Wodak, Shoshana J. |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Proteins Protein binding CAPRI Round 30 Homoprotein Heteroprotein Protein-protein docking Proteïnes--Investigació Àrees temàtiques de la UPC::Enginyeria biomèdica |
| topic |
Proteins Protein binding CAPRI Round 30 Homoprotein Heteroprotein Protein-protein docking Proteïnes--Investigació Àrees temàtiques de la UPC::Enginyeria biomèdica |
| 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. |
| publishDate |
2016 |
| dc.date.none.fl_str_mv |
2016 2016-06-01 2016 2016-11-11 |
| dc.type.none.fl_str_mv |
journal article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/2117/96562 https://dx.doi.org/10.1002/prot.25007 27122118 |
| url |
https://hdl.handle.net/2117/96562 https://dx.doi.org/10.1002/prot.25007 |
| identifier_str_mv |
27122118 |
| dc.language.none.fl_str_mv |
Inglés eng |
| language_invalid_str_mv |
Inglés |
| language |
eng |
| dc.relation.none.fl_str_mv |
European Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 604102 The Human Brain Project European Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 327899 Exploring the evolution of protein-protein interactions and their networks using biophysical models European Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 659025 A dynamical view of binding affinity |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 Attribution-NonCommercial-NoDerivs 4.0 Spain http://creativecommons.org/licenses/by-nc-nd/4.0/es/ |
| dc.rights.openaire.fl_str_mv |
info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 Attribution-NonCommercial-NoDerivs 4.0 Spain http://creativecommons.org/licenses/by-nc-nd/4.0/es/ |
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openAccess |
| dc.format.none.fl_str_mv |
application/pdf |
| dc.publisher.none.fl_str_mv |
Wiley |
| publisher.none.fl_str_mv |
Wiley |
| dc.source.none.fl_str_mv |
reponame:UPCommons. Portal del coneixement obert de la UPC instname:Universitat Politècnica de Catalunya (UPC) |
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Universitat Politècnica de Catalunya (UPC) |
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UPCommons. Portal del coneixement obert de la UPC |
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UPCommons. Portal del coneixement obert de la UPC |
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1869411929176408064 |
| spelling |
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experimentLesink, Marc F.Velankar, SameerKryshtafovych, AndriyHuang, Shen-YouSchneidman-Duhovny, DinaSali, AndrejSegura, JoanFernandez-Fuentes, NarcisShruthi, ViswanathElber, RonGrudinin, SergeiPopov, PetrNeveu, EmilieLee, HasupBaek, MinkyungPark, SangwooHeo, LimLee, Gyu R.Seok, ChaokQin, SanboZhou, Huan-XiangRitchie, David W.Maigret, BernardDevignes, Marie-DominiqueGhoorah, AnisahTorchala, MieczyslawChaleil, Raphaël A.G.Bates, Paul A.Ben-Zeev, EfratEisenstein, MiriamNegi, Surendra S.Weng, ZhipingVreven, ThomPierce, Brian G.Borrman, Tyler M.Yu, JinchaoOchsenbein, FrançoiseGuerois, RaphaëlVangone, AnnaRodrigues, Joao P.G.L.M.Zundert, Gydo vanNellen, MehdiXue, LiKaraca, EzgiMelquiond, Adrien S.J.Visscher, KoenKastritis, Panagiotis L.Bonvin, Alexandre M.J.J.Xianjin, XuQiu, LimingYan, ChengfeiLi, JilongMa, ZhiweiCheng, JianlinZou, XiaoqinShen, YangPeterson, Lenna X.Kim, Hyung-RaeRoy, AmitHan, XusiEsquivel-Rodriguez, JuanKihara, DaisukeYu, XiaofengBruce, Neil J.Fuller, Jonathan C.Wade, Rebecca C.Anishchenko, IvanKundrotas, Petras J.Vakser, Ilya A.Imai, KenichiroYamada, KazunoriOda, ToshiyukiNakamura, TsukasaTomii, KentaroPallara, ChiaraRomero-Durana, MiguelJiménez-García, BrianMoal, Iain H.Fernández-Recio, JuanJoung, Jong Y.Kim, Jong Y.Joo, KeehyoungLee, JooyoungKozakov, DimaVajda, SandorMottarella, ScottHall, David R.Beglov, DmitriMamonov, ArtemXia, BingBohnuud, Tanggisdel Carpio, Carlos A.Ichiishi, EichiroMarze, NicholasKuroda, DaisukeBurman, Shourya S.Gray, Jeffrey J.Chermak, EdrisseCavallo, LuigiOliva, RominaTovchigrechko, AndreyWodak, Shoshana J.ProteinsProtein bindingCAPRI Round 30HomoproteinHeteroproteinProtein-protein dockingProteïnes--InvestigacióÀrees temàtiques de la UPC::Enginyeria biomèdicaWe 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.We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”Peer ReviewedWiley20162016-06-0120162016-11-11journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/96562https://dx.doi.org/10.1002/prot.2500727122118reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengEuropean Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 604102 The Human Brain ProjectEuropean Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 327899 Exploring the evolution of protein-protein interactions and their networks using biophysical modelsEuropean Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 659025 A dynamical view of binding affinityopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivs 4.0 Spainhttp://creativecommons.org/licenses/by-nc-nd/4.0/es/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/965622026-05-27T15:37:01Z |
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15,300719 |