Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

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• 作者：Antonio Rosato¹ ; ² ; ^{rosato@cerm.unifi.it} ; James  ; M. Aramini³ ; Cheryl Arrowsmith⁴ ; Anurag Bagaria⁵ ; ⁶ ; David Baker⁸ ; Andrea Cavalli⁹ ; Jurgen  ; F. Doreleijers¹⁰ ; Alexander Eletsky¹¹ ; Andrea Giachetti¹ ; Paul Guerry¹² ; Aleksandras Gutmanas⁴ ; Peter Gü ; ntert⁵ ; ⁶ ; Yunfen He¹¹ ; Torsten Herrmann¹² ; Yuanpeng  ; J. Huang³ ; Victor Jaravine⁵ ; ⁶ ; Hendrik  ; R.A. Jonker⁶ ; ⁷ ; Michael  ; A. Kennedy¹³ ; Oliver  ; F. Lange⁸ ; Gaohua Liu³ ; Thé ; rè ; se  ; E. Malliavin¹⁴ ; Rajeswari Mani³ ; Binchen Mao³ ; Gaetano  ; T. Montelione³ ; Michael Nilges¹⁴ ; Paolo Rossi³ ; Gijs van  ; der  ; Schot¹⁵ ; Harald Schwalbe⁶ ; ⁷ ; Thomas  ; A. Szyperski¹¹ ; Michele Vendruscolo⁹ ; Robert Vernon⁸ ; Wim  ; F. Vranken¹⁶ ; ¹⁷ ; Sjoerd de  ; Vries¹⁵ ; ¹⁹ ; Geerten  ; W. Vuister¹⁰ ; ¹⁸ ; Bin Wu⁴ ; Yunhuang Yang¹³ ; Alexandre  ; M.J.J. Bonvin¹⁵
• 刊名：Structure
• 出版年：2012
• 出版时间：8 February 2012
• 年：2012
• 卷：20
• 期：2
• 页码：227-236
• 全文大小：528 K

文摘

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Summary

The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (NOESY) peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent ¡°blind?assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR.