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Blind prediction of interfacial water positions in CAPRI

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10.1002/prot.24439
 
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hdl:2117/103445

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Lensink, Marc F.
Moal, Iain H.
Bates, Paul A.
Kastritis, Panagiotis L.
Melquiond, Adrien S.J.
Karaca, Ezgi
Schmitz, Christophe
van Dijk, Marc
Bonvin, Alexandre M.J.J.
Eisenstein, Miriam
Jiménez-Garcia, Brian
Grosdidier, Solène
Solernou, Albert
Pérez-Cano, Laura
Pallara, Chiara
Fernández-Recio, Juan
Xu, Jianqing
Muthu, Pravin
Kilambi, Krishna P.
Gray, Jeffrey J.
Grudinin, Sergei
Derevyanko, Georgy
Mitchell, Julie C.
Wieting, John
Kanamori, Eiji
Tsuchiya, Yuko
Murakami, Yoichi
Sarmiento, Joy
Standley, Daron M.
Shirota, Matsuyuki
Kinoshita, Kengo
Nakamura, Haruki
Chavent, Matthieu
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.
Kleanthous, Colin
Wodak, Shoshana J.
Document typeArticle
Defense date2014-04
PublisherWiley
Rights accessOpen Access
All rights reserved. This work is protected by the corresponding intellectual and industrial property rights. Without prejudice to any existing legal exemptions, reproduction, distribution, public communication or transformation of this work are prohibited without permission of the copyright holder
Abstract
We 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.
Description
This 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.
CitationLensink, M. F. [et al.]. Blind prediction of interfacial water positions in CAPRI. "Proteins", Abril 2014, vol. 82, núm. 4, p. 620-632. 
URIhttp://hdl.handle.net/2117/103445
DOI10.1002/prot.24439
ISSN0887-3585
Publisher versionhttp://onlinelibrary.wiley.com/doi/10.1002/prot.24439/abstract
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