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dc.contributor.authorKundrotas, Petras J.
dc.contributor.authorVakser, Ilya A.
dc.date.accessioned2017-03-28T19:21:16Z
dc.date.available2017-03-28T19:21:16Z
dc.date.issued2014-04
dc.identifier.citationLensink, M. F., Moal, I. H., Bates, P. A., Kastritis, P. L., Melquiond, A. S. J., Karaca, E., … Wodak, S. J. (2014). Blind Prediction of Interfacial Water Positions in CAPRI. Proteins, 82(4), 620–632. http://doi.org/10.1002/prot.24439en_US
dc.identifier.urihttp://hdl.handle.net/1808/23505
dc.description.abstractWe report the first assessment of blind predictions of water positions at protein-protein interfaces, performed as part of the CAPRI (Critical Assessment of Predicted Interactions) 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 Å, 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 high quality 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.en_US
dc.publisherWileyen_US
dc.rightsThis is the peer reviewed version of the following article: Proteins, which has been published in final form at http://dx.doi.org/10.1002/prot.24439. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.en_US
dc.subjectProtein dockingen_US
dc.subjectWateren_US
dc.subjectBlind predictionen_US
dc.subjectCAPRIen_US
dc.subjectProtein interfaceen_US
dc.titleBlind Prediction of Interfacial Water Positions in CAPRIen_US
dc.typeArticleen_US
kusw.kuauthorKundrotas, Petras J.
kusw.kuauthorVasker, Ilya A.
kusw.kudepartmentMolecular Biosciencesen_US
dc.identifier.doi10.1002/prot.24439en_US
kusw.oaversionScholarly/refereed, author accepted manuscripten_US
kusw.oapolicyThis item meets KU Open Access policy criteria.en_US
dc.rights.accessrightsopenAccess


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