Blind testing of routine, fully automated determination of protein structures from NMR data.

TitleBlind testing of routine, fully automated determination of protein structures from NMR data.
Publication TypeJournal Article
Year of Publication2012
AuthorsRosato, A., J. M. Aramini, C. Arrowsmith, A. Bagaria, D. Baker, A. Cavalli, J. F. Doreleijers, A. Eletsky, A. Giachetti, P. Guerry, A. Gutmanas, P. G√ľntert, Y. He, T. Herrmann, Y. J. Huang, V. Jaravine, H. R. A. Jonker, M. A. Kennedy, O. F. Lange, G. Liu, T. E. Malliavin, R. Mani, B. Mao, G. T. Montelione, M. Nilges, P. Rossi, G. van der Schot, H. Schwalbe, T. A. Szyperski, M. Vendruscolo, R. Vernon, W. F. Vranken, S. de Vries, G. W. Vuister, B. Wu, Y. Yang, and A. M. J. J. Bonvin
JournalStructure
Volume20
Issue2
Pagination227-36
Date Published2012 Feb 8
ISSN1878-4186
KeywordsAutomatic Data Processing, Automation, Laboratory, Data Interpretation, Statistical, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Proteins, Research Design, Software
Abstract

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.

DOI10.1016/j.str.2012.01.002
Alternate JournalStructure
PubMed ID22325772
PubMed Central IDPMC3609704
Grant ListBB/J007897/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
U54 GM074958 / GM / NIGMS NIH HHS / United States
U54 GM094597 / GM / NIGMS NIH HHS / United States
U54 GM094597 / GM / NIGMS NIH HHS / United States
U54 GM094597-02 / GM / NIGMS NIH HHS / United States
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