NDLI: Blind Prediction of Interfacial Water Positions in CAPRI

Content Provider	PubMed Central
Author	Lensink, Marc F. Moal, Iain H. Bates, Paul A. Kastritis, Panagiotis L. Melquiond, Adrien S. J. Karaca, Ezgi Schmitz, Christophe Dijk, Marc Van Bonvin, Alexandre M. J. J. Eisenstein, Miriam Brian, Jiménez-garcía Grosdidier, Solène Solernou, Albert Laura, Pérez-cano Chiara, Pallara Juan, Fernández-recio Xu, Jianqing Muthu, Pravin Kilambi, Krishna Praneeth Gray, Jeffrey J. Sergei, Grudinin Derevyanko, Georgy Mitchell, Julie C. Wieting, John Kanamori, Eiji Tsuchiya, Yuko Murakami, Yoichi Sarmiento, Joy Standley, Daron M. Shirota, Matsuyuki Kinoshita, Kengo Nakamura, Haruki Matthieu, Chavent Ritchie, David W. Park, Hahnbeom Ko, Junsu Lee, Hasup Seok, Chaok Shen, Yang Kozakov, Dima Vajda, Sandor Kundrotas, Petras J. Vakser, Ilya A. Pierce, Brian G. Hwang, Howook Vreven, Thom Weng, Zhiping Buch, Idit Farkash, Efrat Wolfson, Haim J. Zacharias, Martin Qin, Sanbo Zhou, Huan-xiang Huang, Shen-you Zou, Xiaoqin Wojdyla, Justyna A. Colin, Kleanthous Wodak, Shoshana J.
Abstract	We 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.
Related Links	http://dx.doi.org/10.1002/prot.24439
Ending Page	632
Page Count	13
Starting Page	620
File Format	PDF
ISSN	08873585
e-ISSN	10970134
Journal	Proteins
Issue Number	4
Volume Number	82
Language	English
Publisher Date	2014-04-01
Access Restriction	Open
Subject Keyword	Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Structural Biology Biochemistry Molecular Biology

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