A generalized approach to automated NMR peak list editing: application to reduced dimensionality triple resonance spectra

Journal of Magnetic Resonance
Hunter N B MoseleyGaetano T Montelione

Abstract

We present an algorithm and program called Pattern Picker that performs editing of raw peak lists derived from multidimensional NMR experiments with characteristic peak patterns. Pattern Picker detects groups of correlated peaks within peak lists from reduced dimensionality triple resonance (RD-TR) NMR spectra, with high fidelity and high yield. With typical quality RD-TR NMR data sets, Pattern Picker performs almost as well as human analysis, and is very robust in discriminating real peak sets from noise and other artifacts in unedited peak lists. The program uses a depth-first search algorithm with short-circuiting to efficiently explore a search tree representing every possible combination of peaks forming a group. The Pattern Picker program is particularly valuable for creating an automated peak picking/editing process. The Pattern Picker algorithm can be applied to a broad range of experiments with distinct peak patterns including RD, G-matrix Fourier transformation (GFT) NMR spectra, and experiments to measure scalar and residual dipolar coupling, thus promoting the use of experiments that are typically harder for a human to analyze. Since the complexity of peak patterns becomes a benefit rather than a drawback, Pattern P...Continue Reading

References

Jul 1, 1991·Journal of Biomolecular NMR·C EcclesK Wüthrich
May 1, 1994·Journal of Biomolecular NMR·J P SimorreD Marion
Nov 1, 1995·Journal of Biomolecular NMR·F DelaglioA Bax
May 8, 1998·Journal of Magnetic Resonance·M OttigerA Bax
Jan 8, 1999·Journal of Magnetic Resonance·R KoradiK Wüthrich
Oct 6, 1999·Current Opinion in Structural Biology·H N Moseley, G T Montelione
Dec 5, 2000·Nature Structural Biology·G T MontelioneT Szyperski
Jul 27, 2001·Biochemistry·J H PrestegardF Tian
Oct 5, 2001·Nature Reviews. Genetics·S E Brenner
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Thomas SzyperskiGaetano T Montelione
Jan 30, 2003·Journal of the American Chemical Society·Seho Kim, Thomas Szyperski
Mar 12, 2003·Journal of Molecular Biology·Yuanpeng Janet HuangGaetano T Montelione
Feb 3, 2004·Journal of Biomolecular NMR·Seho Kim, Thomas Szyperski

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Citations

Sep 23, 2008·European Biophysics Journal : EBJ·Peter Güntert
Apr 11, 2006·Journal of Biomolecular NMR·Brian E Coggins, Pei Zhou
Sep 9, 2008·Journal of Biomolecular NMR·Doroteya K StaykovaMartin Billeter
Oct 9, 2008·Journal of Biomolecular NMR·Sebastian HillerKurt Wüthrich
Jan 13, 2009·Journal of Biomolecular NMR·Mike P Williamson, C Jeremy Craven
Mar 25, 2009·Journal of Biomolecular NMR·Geoffrey A Mueller
Jul 19, 2012·Journal of Biomolecular NMR·Jonas FredrikssonMartin Billeter
Mar 17, 2009·Journal of Structural and Functional Genomics·Gaetano T MontelioneThomas Szyperski
Jun 6, 2009·Journal of Structural and Functional Genomics·Yibing WuThomas Szyperski
Jul 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·Sebastian HillerGerhard Wider
Oct 7, 2009·Journal of Magnetic Resonance·Hyung-Won KohLars Hildebrand
Jun 24, 2005·Journal of Magnetic Resonance·Daniel Malmodin, Martin Billeter
Jul 11, 2006·Magnetic Resonance in Chemistry : MRC·Rochus KellerRoland Riek
Jul 11, 2006·Magnetic Resonance in Chemistry : MRC·Daniel Malmodin, Martin Billeter
Jul 11, 2006·Magnetic Resonance in Chemistry : MRC·Thomas Szyperski, Hanudatta S Atreya
Jan 14, 2009·Angewandte Chemie·Yibing WuThomas Szyperski
Jun 9, 2015·Magnetic Resonance in Chemistry : MRC·Andrés M CastilloJulien Wist

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