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dc.contributor.authorLensink, Marc F.
dc.contributor.authorMoal, Iain H.
dc.contributor.authorBates, Paul A.
dc.contributor.authorKastritis, Panagiotis L.
dc.contributor.authorMelquiond, Adrien S.J.
dc.contributor.authorKaraca, Ezgi
dc.contributor.authorSchmitz, Christophe
dc.contributor.authorvan Dijk, Marc
dc.contributor.authorBonvin, Alexandre M.J.J.
dc.contributor.authorEisenstein, Miriam
dc.contributor.authorJiménez-Garcia, Brian
dc.contributor.authorGrosdidier, Solène
dc.contributor.authorSolernou, Albert
dc.contributor.authorPérez-Cano, Laura
dc.contributor.authorPallara, Chiara
dc.contributor.authorFernández-Recio, Juan
dc.contributor.authorXu, Jianqing
dc.contributor.authorMuthu, Pravin
dc.contributor.authorKilambi, Krishna P.
dc.contributor.authorGray, Jeffrey J.
dc.contributor.authorGrudinin, Sergei
dc.contributor.authorDerevyanko, Georgy
dc.contributor.authorMitchell, Julie C.
dc.contributor.authorWieting, John
dc.contributor.authorKanamori, Eiji
dc.contributor.authorTsuchiya, Yuko
dc.contributor.authorMurakami, Yoichi
dc.contributor.authorSarmiento, Joy
dc.contributor.authorStandley, Daron M.
dc.contributor.authorShirota, Matsuyuki
dc.contributor.authorKinoshita, Kengo
dc.contributor.authorNakamura, Haruki
dc.contributor.authorChavent, Matthieu
dc.contributor.authorRitchie, David W.
dc.contributor.authorPark, Hahnbeom
dc.contributor.authorKo, Junsu
dc.contributor.authorLee, Hasup
dc.contributor.authorSeok, Chaok
dc.contributor.authorShen, Yang
dc.contributor.authorKozakov, Dima
dc.contributor.authorVajda, Sandor
dc.contributor.authorKundrotas, Petras J.
dc.contributor.authorVakser, Ilya A.
dc.contributor.authorPierce, Brian G.
dc.contributor.authorHwang, Howook
dc.contributor.authorVreven, Thom
dc.contributor.authorWeng, Zhiping
dc.contributor.authorBuch, Idit
dc.contributor.authorFarkash, Efrat
dc.contributor.authorWolfson, Haim J.
dc.contributor.authorZacharias, Martin
dc.contributor.authorQin, Sanbo
dc.contributor.authorZhou, Huan-Xiang
dc.contributor.authorHuang, Shen-You
dc.contributor.authorZou, Xiaoqin
dc.contributor.authorWojdyla, Justyna A.
dc.contributor.authorKleanthous, Colin
dc.contributor.authorWodak, Shoshana J.
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2017-04-07T10:19:12Z
dc.date.available2017-04-07T10:19:12Z
dc.date.issued2014-04
dc.identifier.citationLensink, M. F. [et al.]. Blind prediction of interfacial water positions in CAPRI. "Proteins", Abril 2014, vol. 82, núm. 4, p. 620-632.
dc.identifier.issn0887-3585
dc.identifier.urihttp://hdl.handle.net/2117/103445
dc.descriptionThis is the peer reviewed version of the following article: [Lensink, M. F., Moal, I. H., Bates, P. A., Kastritis, P. L., Melquiond, A. S. J., Karaca, E., Schmitz, C., van Dijk, M., Bonvin, A. M. J. J., Eisenstein, M., Jiménez-García, B., Grosdidier, S., Solernou, A., Pérez-Cano, L., Pallara, C., Fernández-Recio, J., Xu, J., Muthu, P., Praneeth Kilambi, K., Gray, J. J., Grudinin, S., Derevyanko, G., Mitchell, J. C., Wieting, J., Kanamori, E., Tsuchiya, Y., Murakami, Y., Sarmiento, J., Standley, D. M., Shirota, M., Kinoshita, K., Nakamura, H., Chavent, M., Ritchie, D. W., Park, H., Ko, J., Lee, H., Seok, C., Shen, Y., Kozakov, D., Vajda, S., Kundrotas, P. J., Vakser, I. A., Pierce, B. G., Hwang, H., Vreven, T., Weng, Z., Buch, I., Farkash, E., Wolfson, H. J., Zacharias, M., Qin, S., Zhou, H.-X., Huang, S.-Y., Zou, X., Wojdyla, J. A., Kleanthous, C. and Wodak, S. J. (2014), Blind prediction of interfacial water positions in CAPRI. Proteins, 82: 620–632. doi:10.1002/prot.24439], which has been published in final form at [Link to final article using the 10.1002/prot.24439]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
dc.description.abstractWe report the first assessment of blind predictions of water positions at protein–protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting docking predictions for the complex of the DNase domain of colicin E2 and Im2 immunity protein (CAPRI Target 47), were invited to predict the positions of interfacial water molecules using the method of their choice. The predictions—20 groups submitted a total of 195 models—were assessed by measuring the recall fraction of water-mediated protein contacts. Of the 176 high- or medium-quality docking models—a very good docking performance per se—only 44% had a recall fraction above 0.3, and a mere 6% above 0.5. The actual water positions were in general predicted to an accuracy level no better than 1.5 A °, and even in good models about half of the contacts represented false positives. This notwithstanding, three hotspot interface water positions were quite well predicted, and so was one of the water positions that is believed to stabilize the loop that confers specificity in these complexes. Overall the best interface water predictions was achieved by groups that also produced highquality docking models, indicating that accurate modelling of the protein portion is a determinant factor. The use of established molecular mechanics force fields, coupled to sampling and optimization procedures also seemed to confer an advantage. Insights gained from this analysis should help improve the prediction of protein–water interactions and their role in stabilizing protein complexes.
dc.description.sponsorshipThe Canadian Institutes for Health Research is gratefully acknowledged for support to SJW. MFL acknowledges financial support from the French Agence Nationale de Recherche (grant ANR-12-BSV5-0009-01, Fluctuations in Structured Coulomb Fluids). (Vakser): IAV and PJK are supported by NIH grant R01GM074255. CK acknowledges support for this work from the BBSRC (grant GG/G020671/1).
dc.format.extent13 p.
dc.language.isoeng
dc.publisherWiley
dc.subjectÀrees temàtiques de la UPC::Enginyeria biomèdica
dc.subject.lcshProtein interactions
dc.subject.lcshProteins--Analysis
dc.subject.lcshWater
dc.subject.otherProtein docking
dc.subject.otherWater
dc.subject.otherBlind prediction
dc.subject.otherCAPRI
dc.subject.otherProtein interface
dc.titleBlind prediction of interfacial water positions in CAPRI
dc.typeArticle
dc.subject.lemacProteïnes--Anàlisi
dc.subject.lemacAigua--Anàlisi
dc.identifier.doi10.1002/prot.24439
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttp://onlinelibrary.wiley.com/doi/10.1002/prot.24439/abstract
dc.rights.accessOpen Access
dc.description.versionPostprint (author's final draft)
local.citation.publicationNameProteins
local.citation.volume82
local.citation.number4
local.citation.startingPage620
local.citation.endingPage632


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