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dc.contributor.authorLesink, Marc F.
dc.contributor.authorVelankar, Sameer
dc.contributor.authorKryshtafovych, Andriy
dc.contributor.authorHuang, Shen-You
dc.contributor.authorSchneidman-Duhovny, Dina
dc.contributor.authorSali, Andrej
dc.contributor.authorSegura, Joan
dc.contributor.authorFernandez-Fuentes, Narcis
dc.contributor.authorShruthi, Viswanath
dc.contributor.authorElber, Ron
dc.contributor.authorGrudinin, Sergei
dc.contributor.authorPopov, Petr
dc.contributor.authorNeveu, Emilie
dc.contributor.authorLee, Hasup
dc.contributor.authorBaek, Minkyung
dc.contributor.authorPark, Sangwoo
dc.contributor.authorHeo, Lim
dc.contributor.authorLee, Gyu R.
dc.contributor.authorSeok, Chaok
dc.contributor.authorQin, Sanbo
dc.contributor.authorZhou, Huan-Xiang
dc.contributor.authorRitchie, David W.
dc.contributor.authorMaigret, Bernard
dc.contributor.authorDevignes, Marie-Dominique
dc.contributor.authorGhoorah, Anisah
dc.contributor.authorTorchala, Mieczyslaw
dc.contributor.authorChaleil, Raphaël A.G.
dc.contributor.authorBates, Paul A.
dc.contributor.authorBen-Zeev, Efrat
dc.contributor.authorEisenstein, Miriam
dc.contributor.authorNegi, Surendra S.
dc.contributor.authorWeng, Zhiping
dc.contributor.authorVreven, Thom
dc.contributor.authorPierce, Brian G.
dc.contributor.authorBorrman, Tyler M.
dc.contributor.authorYu, Jinchao
dc.contributor.authorOchsenbein, Françoise
dc.contributor.authorGuerois, Raphaël
dc.contributor.authorVangone, Anna
dc.contributor.authorRodrigues, Joao P.G.L.M.
dc.contributor.authorZundert, Gydo van
dc.contributor.authorNellen, Mehdi
dc.contributor.authorXue, Li
dc.contributor.authorKaraca, Ezgi
dc.contributor.authorMelquiond, Adrien S.J.
dc.contributor.authorVisscher, Koen
dc.contributor.authorKastritis, Panagiotis L.
dc.contributor.authorBonvin, Alexandre M.J.J.
dc.contributor.authorXianjin, Xu
dc.contributor.authorQiu, Liming
dc.contributor.authorYan, Chengfei
dc.contributor.authorLi, Jilong
dc.contributor.authorMa, Zhiwei
dc.contributor.authorCheng, Jianlin
dc.contributor.authorZou, Xiaoqin
dc.contributor.authorShen, Yang
dc.contributor.authorPeterson, Lenna X.
dc.contributor.authorKim, Hyung-Rae
dc.contributor.authorRoy, Amit
dc.contributor.authorHan, Xusi
dc.contributor.authorEsquivel-Rodriguez, Juan
dc.contributor.authorKihara, Daisuke
dc.contributor.authorYu, Xiaofeng
dc.contributor.authorBruce, Neil J.
dc.contributor.authorFuller, Jonathan C.
dc.contributor.authorWade, Rebecca C.
dc.contributor.authorAnishchenko, Ivan
dc.contributor.authorKundrotas, Petras J.
dc.contributor.authorVakser, Ilya A.
dc.contributor.authorImai, Kenichiro
dc.contributor.authorYamada, Kazunori
dc.contributor.authorOda, Toshiyuki
dc.contributor.authorNakamura, Tsukasa
dc.contributor.authorTomii, Kentaro
dc.contributor.authorPallara, Chiara
dc.contributor.authorRomero-Durana, Miguel
dc.contributor.authorJiménez-García, Brian
dc.contributor.authorMoal, Iain H.
dc.contributor.authorFernández-Recio, Juan
dc.contributor.authorJoung, Jong Y.
dc.contributor.authorKim, Jong Y.
dc.contributor.authorJoo, Keehyoung
dc.contributor.authorLee, Jooyoung
dc.contributor.authorKozakov, Dima
dc.contributor.authorVajda, Sandor
dc.contributor.authorMottarella, Scott
dc.contributor.authorHall, David R.
dc.contributor.authorBeglov, Dmitri
dc.contributor.authorMamonov, Artem
dc.contributor.authorXia, Bing
dc.contributor.authorBohnuud, Tanggis
dc.contributor.authordel Carpio, Carlos A.
dc.contributor.authorIchiishi, Eichiro
dc.contributor.authorMarze, Nicholas
dc.contributor.authorKuroda, Daisuke
dc.contributor.authorBurman, Shourya S.
dc.contributor.authorGray, Jeffrey J.
dc.contributor.authorChermak, Edrisse
dc.contributor.authorCavallo, Luigi
dc.contributor.authorOliva, Romina
dc.contributor.authorTovchigrechko, Andrey
dc.contributor.authorWodak, Shoshana J.
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2016-11-11T13:55:59Z
dc.date.available2016-11-11T13:55:59Z
dc.date.issued2016-06-01
dc.identifier.citationLesink, Marc F. [et al.]. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. "Proteins: Structure, Function, and Bioinformatics", 1 Juny 2016, vol. 84, núm. 1, p. 323-348.
dc.identifier.issn0887-3585
dc.identifier.urihttp://hdl.handle.net/2117/96562
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.
dc.description.sponsorshipWe 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.”
dc.format.extent26 p.
dc.language.isoeng
dc.publisherWiley
dc.rightsAttribution-NonCommercial-NoDerivs 4.0 Spain
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/es/
dc.subjectÀrees temàtiques de la UPC::Enginyeria biomèdica
dc.subject.lcshProteins
dc.subject.lcshProtein binding
dc.subject.otherCAPRI Round 30
dc.subject.otherHomoprotein
dc.subject.otherHeteroprotein
dc.subject.otherProtein-protein docking
dc.titlePrediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
dc.typeArticle
dc.subject.lemacProteïnes--Investigació
dc.identifier.doi10.1002/prot.25007
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttp://onlinelibrary.wiley.com/doi/10.1002/prot.25007/full
dc.rights.accessOpen Access
dc.description.versionPostprint (published version)
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/FP7/604102/EU/The Human Brain Project/HBP
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/FP7/327899/EU/Exploring the evolution of protein-protein interactions and their networks using biophysical models/EEPPIBM
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/659025/EU/A dynamical view of binding affinity/BAP
local.citation.publicationNameProteins: Structure, Function, and Bioinformatics
local.citation.volume84
local.citation.number1
local.citation.startingPage323
local.citation.endingPage348
dc.identifier.pmid27122118


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