Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA

Journal of Biomolecular NMR
Lena Buchner, Peter Güntert

Abstract

The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment and structure calculation with CYANA under a variety of conditions on the basis of the experimental NMR data sets of ten proteins. To evaluate the robustness of the algorithm, the original high-quality experimental data sets were modified in different ways to simulate the effect of data imperfections, i.e. incomplete or erroneous chemical shift assignments, missing NOESY cross peaks, inaccurate peak positions, inaccurate peak intensities, lower dimensionality NOESY spectra, and higher tolerances for the matching of chemical shifts and peak positions. The results show that the algorithm is remarkably robust with regard to imperfections of the NOESY peak lists and the chemical shift tolerances but susceptible to lacking or erroneous resonance assignments, in particular for nuclei that a...Continue Reading

References

Aug 1, 1996·Nature Structural Biology·W AntuchK Wüthrich
Nov 21, 1997·Journal of Molecular Biology·P GüntertK Wüthrich
Feb 14, 1998·Journal of Biomolecular NMR·C MumenthalerK Wüthrich
Oct 30, 1998·Quarterly Reviews of Biophysics·P Güntert
Jul 31, 1999·The Journal of Biological Chemistry·R WimmerK Wüthrich
Oct 6, 1999·Current Opinion in Structural Biology·H N Moseley, G T Montelione
May 24, 2001·Journal of Biomolecular NMR·B M DugganP E Wright
Nov 29, 2001·Proceedings of the National Academy of Sciences of the United States of America·R HorstK Wüthrich
Oct 26, 2002·Journal of Biomolecular NMR·Wolfram GronwaldHans Robert Kalbitzer
Dec 3, 2003·Journal of Structural and Functional Genomics·JunGoo Jee, Peter Güntert
Mar 12, 2004·Journal of Biomolecular NMR·Blanca López-MéndezPeter Güntert
Mar 12, 2004·Journal of Biomolecular NMR·David Pantoja-UcedaPeter Güntert
Aug 12, 2004·Chemical Reviews·Michael C BaranGaetano T Montelione
Oct 7, 2004·Current Opinion in Structural Biology·Amanda S Altieri, R Andrew Byrd
Dec 4, 2004·Protein Science : a Publication of the Protein Society·David Pantoja-UcedaPeter Güntert
Jan 5, 2005·Journal of Biomolecular NMR·Anna ScottPeter Güntert
Jan 14, 2005·Proceedings of the National Academy of Sciences of the United States of America·Luigi CalzolaiKurt Wüthrich
Jun 2, 2005·Journal of Biomolecular NMR·Anna ScottPeter Güntert
Feb 8, 2006·PLoS Computational Biology·Sander B NabuursGert Vriend
Mar 3, 2006·Nature·Masatsune KainoshoPeter Güntert
Jun 1, 2006·Proteins·Kimmo PääkkönenPeter Güntert
Oct 4, 2006·Journal of Biomolecular NMR·Ling-Hong Hung, Ram Samudrala
Oct 5, 2006·Journal of the American Chemical Society·Blanca López-Méndez, Peter Güntert
Nov 24, 2006·Bioinformatics·Wolfgang RiepingMichael Nilges
Jan 24, 2007·FEBS Letters·Satoshi OhnishiShigeyuki Yokoyama
Sep 23, 2008·European Biophysics Journal : EBJ·Peter Güntert
Oct 2, 2008·Journal of Biomolecular NMR·Martin BilleterKurt Wüthrich
Jan 13, 2009·Journal of Biomolecular NMR·Mike P Williamson, C Jeremy Craven
Sep 1, 2009·Nature Methods·Antonio RosatoAlexandre M J J Bonvin
Nov 7, 2009·Journal of the American Chemical Society·Beat VögeliRoland Riek
Mar 18, 2011·Quarterly Reviews of Biophysics·Paul Guerry, Torsten Herrmann
Mar 31, 2011·Journal of Biomolecular NMR·Teppei IkeyaPeter Güntert
May 20, 2011·BMC Bioinformatics·Donata K Kirchner, Peter Güntert
Jul 17, 2012·Journal of the American Chemical Society·Elena Schmidt, Peter Güntert
Sep 4, 2012·Nature Structural & Molecular Biology·Beat VögeliRoland Riek
May 23, 2014·Journal of Biomolecular NMR·Zaiyong ZhangOliver F Lange

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Citations

Mar 25, 2015·Journal of Biomolecular NMR·Peter Güntert, Lena Buchner
Sep 27, 2008·PLoS Computational Biology·Phineus R L MarkwickMichael Nilges
Jul 14, 2009·PLoS Pathogens·Konstantin PervushinJaume Torres
Oct 17, 2013·PloS One·Alexander LemakCheryl H Arrowsmith
Jun 15, 2016·Proceedings of the National Academy of Sciences of the United States of America·Qin ShuCarl Frieden
Jun 8, 2011·PloS One·Kazuhide Miyamoto, Kayo Togiya
Aug 5, 2016·Proceedings of the National Academy of Sciences of the United States of America·Loren B AndreasGuido Pintacuda
Nov 9, 2010·Biochemical and Biophysical Research Communications·Qingxin LiCongbao Kang
Dec 23, 2006·Chemistry & Biology·Pilgrim J JacksonGlenn L Millhauser
Aug 16, 2011·FEBS Letters·Mikaël FeracciFrançoise Guerlesquin
Sep 11, 2007·Biophysical Journal·Ho Ki FungDimitrios Morikis
Dec 21, 2010·Journal of Molecular Biology·Benjamin Chagot, Walter J Chazin
Nov 20, 2016·The Journal of Biological Chemistry·Martin PomsOliver Zerbe
Feb 6, 2017·Journal of Biomolecular NMR·Julia M Würz, Peter Güntert
Mar 16, 2017·Journal of Biomolecular NMR·Qi GaoJames H Prestegard
Jun 20, 2018·Journal of Magnetic Resonance·Joel Lapin, Alexander A Nevzorov
Oct 11, 2017·Biochimica Et Biophysica Acta. Biomembranes·Mukesh MahajanSurajit Bhattacharjya
Jul 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Emel Maden YılmazŞima Etaner-Uyar
Feb 8, 2019·The Journal of Physical Chemistry. B·Conan K Wang, David J Craik

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