Automated Peak Picking and Peak Integration in Macromolecular NMR Spectra Using AUTOPSY

Journal of Magnetic Resonance

Volumn 135, Issue 2, 1998, Pages 288-297

  Koradi, Reto ^a,b   Billeter, Martin ^a,c   Engeli, Max ^a   Güntert, Peter ^a   Wüthrich, Kurt ^a  

^a ETH ZURICH   (Switzerland)

^b TRIPOS INC   (United States)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

AUTOPSY; Lineshapes; Noise level calculation; Peak integration; Peak picking

Indexed keywords

FUNGAL PROTEIN; KILLER FACTOR, YEAST; MYCOTOXIN;

ALGORITHM; ARTICLE; ARTIFACT; IMAGE PROCESSING; MACROMOLECULE; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION;

ALGORITHMS; ARTIFACTS; FUNGAL PROTEINS; IMAGE PROCESSING, COMPUTER-ASSISTED; MACROMOLECULAR SUBSTANCES; MAGNETIC RESONANCE SPECTROSCOPY; MYCOTOXINS; PROTEIN CONFORMATION;

EID: 0032247126     PISSN: 10907807     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmre.1998.1570     Document Type: Article

References (31)

1. K. Wüthrich, "NMR of Proteins and Nucleic Acids," Wiley, New York (1986).
2. K. Wüthrich, "NMR in Structural Biology," World Scientific, Singapore (1995).
3. C. Bartels, T. Xia, M. Billeter, P. Güntert, and K. Wüthrich, The program XEASY for computer-supported NMR spectral analysis of biological macromolecules, J. Biol. NMR 6, 1-10 (1995).
4. K. P. Neidig, M. Geyer, A. Görler, C. Antz, R. Saffrich, W. Beneicke, and H. R. Kalbitzer, AURELIA, a program for computer-aided analysis of multidimensional NMR spectra, J. Biomol. NMR 6, 255-270 (1995).
5. S. A. Corne and P. Johnson, An artificial neural network for classifying cross peaks in two-dimensional NMR spectra, J. Magn. Reson. 100, 256-266 (1992).
6. E. A. Carrara, F. Pagliari, and C. Nicolini, Neural networks for the peak-picking of nuclear magnetic resonance spectra, Neural Networks 6, 1023-1032 (1993).
7. A. Rouh, A. Louis-Joseph, and J.-Y. Lallemand, Bayesian signal extraction from noisy FT NMR spectra, J. Biomol. NMR 4, 505-518 (1994).
8. C. Antz, K.-P. Neidig, and H. R. Kalbitzer, A general Bayesian method for an automated signal class recognition in 2D NMR spectra combined with a mulitivariate discriminant analysis, J. Biomol. NMR 5, 287-296 (1995).
9. 1H NMR spectra, J. Magn. Reson. 88, 601-608 (1990).
10. D. S. Garret, R. Powers, A. M. Gronenborn, and G. M. Clore, A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams, J. Magn. Reson. 95, 214-220 (1991).
11. W. Denk, R. Baumann, and G. Wagner, Quantitative evaluation of cross-peak intensities by projection of two-dimensional NOE spectra on a linear space spanned by a set of reference resonance lines, J. Magn. Reson. 67, 617-636 (1986).
12. T. A. Holak, J. N. Scarsdale, and J. H. Prestegard, A simple method for quantitative evaluation of cross-peak intensities in two-dimensional NOE spectra, J. Magn. Reson. 74, 546-549 (1987).
13. H. Gesmar, P. Fæster Nielsen, and J. J. Led, Simple least-squares estimation of intensities of overlapping signals in 2D NMR spectra, J. Magn. Reson. B 103, 10-18 (1994).
14. J. W. Brown and W. H. Huestis, Quantification of two-dimensional NOE spectra via a combined linear and nonlinear least-squares fit, J. Biomol. NMR 4, 645-652 (1994).
15. K.-H. Sze, I. L. Barsukov, and C. K. Roberts, Quantitative evaluation of cross-peak volumes in multidimensional spectra by nonlinear-least-squares curve fitting, J. Magn. Reson. A 113, 185-195 (1995).
16. B. U. Meier, G. Bodenhausen, and R. R. Ernst, Pattern recognition in two-dimensional NMR spectra, J. Magn. Reson. 60, 161-163 (1984).
17. K. P. Neidig, R. Saffrich, M. Lorenz, and H. R. Kalbitzer, Cluster analysis and multiplet pattern recognition in two-dimensional NMR spectra, J. Magn. Reson. 89, 543-552 (1990).
18. D. Jeannerat and G. Bodenhausen, Separation of overlapping multiplets and contraction of substructures within multiplets using symmetry properties, J. Magn. Reson. A 119, 139-144 (1996).
19. P. Solé, F. Delaglio, and G. C. Levy, A segmentation technique for automated contour selection in 2D NMR spectroscopy, J. Magn. Reson. 80, 517-519 (1988).
20. J. D. Foley, A. van Dam, S. K. Feiner, and J. F. Hughes, "Computer Graphics: Principles and Practice," pp. 689-693, Addison-Wesley, Reading (1990).
21. R. Baumann, G. Wider, R. R. Ernst, and K. Wüthrich, Improvement of 2D NOE and 2D correlated spectra by symmetrization, J. Magn. Reson. 44, 402-406 (1981).
22. C. Rischel, P. Osmark, and F. M. Poulsen, Resolving overlaps in two-dimensional NOE spectra by cross-peak subtraction, J. Magn. Reson. B 110, 80-81 (1996).
23. R. Sedgewick, "Algorithms," pp. 380-386, Addison-Wesley, Reading (1988).
24. W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling, "Numerical Recipes in C," Cambridge Univ. Press, Cambridge, United Kingdom (1988).
25. R. Koradi, M. Billeter, and K. Wüthrich, MOLMOL: A program for display and analysis of macromolecular structures, J. Mol. Graphics 14, 51-55 (1996).
26. W. Antuch, P. Güntert, and K. Wüthrich, Ancestral βγ-crystallin percursor structure in a yeast killer toxin, Nature Struct. Biol. 3, 662-665 (1996).
27. C. Mumenthaler, P. Güntert, W. Braun, and K. Wüthrich, Automated combined assignment of NOESY spectra and three-dimensional protein structure determination, J. Biomol. NMR 10, 351-362 (1997).
28. P. Güntert, C. Mumenthaler, and K. Wüthrich, Torsion angle dynamics for NMR structure calculation with the new program DYANA, J. Mol. Biol. 273, 283-298 (1997).
29. C. Mumenthaler and W. Braun, Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry, J. Mol. Biol. 254, 465-480 (1995).
30. C. Bartels, P. Güntert, M. Billeter, and K. Wüthrich, GARANT - A general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra, J. Comp. Chem. 18, 139-149 (1997).
31. P. Güntert, W. Braun, and K. Wüthrich, Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA, J. Mol. Biol. 217, 517-530 (1991).