Using NMRView to Visualize and Analyze the NMR Spectra of Macromolecules

  • Bruce A. Johnson
Part of the Methods in Molecular Biology™ book series (MIMB, volume 278)

Abstract

Nuclear magnetic resonance (NMR) experiments on macromolecules can generate a tremendous amount of data that must be analyzed and correlated to generate conclusions about the structure and dynamics of the molecular system. NMRView is a computer program that is designed to be useful in visualizing and analyzing these data. NMRView works with various types of NMR datasets and can have multiple datasets and display windows opened simultaneously. Virtually all actions of the program can be controlled through the Tcl scripting language, and new graphical user interface components can be added with the Tk toolkit. NMR spectral peaks can be analyzed and assigned. A suite of tools exists within NMRView for assigning the data from triple-resonance experiments.

Key Words

NMR computer software assignment chemical shift NOE spectrum 

References

  1. 1.
    Johnson, B. A. and Blevins, R. A. (1994) NMRView: a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603–614.CrossRefGoogle Scholar
  2. 2.
    Bartels, C., Xia, T. H., Billeter, M., Güntert, P., and Wüthrich, K. (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR 6, 1–10.CrossRefGoogle Scholar
  3. 3.
    Goddard, T. D. and Kneller, D. G. (2001) Sparky 3. University of California, San Francisco.Google Scholar
  4. 4.
    Hoch, J. C. (1985) Rowland NMR Toolkit. Rowland Institute, Harvard University, Cambridge, MA.Google Scholar
  5. 5.
    Pons, J. L., Malliavin, T. E., and Delsuc, M. A. (1996) Gifa V 4: a complete package for NMR data set processing. J. Biomol. NMR 8, 445–452.PubMedCrossRefGoogle Scholar
  6. 6.
    Kjaer, M., Andersen, K. V., and Poulsen, F. M. (1994) Automated and semiautomated analysis of homo-and heteronuclear multidimensional nuclear magnetic resonance spectra of proteins: the program Pronto. Methods Enzymol. 239, 288–307.PubMedCrossRefGoogle Scholar
  7. 7.
    Ousterhout, J. (1994) Tcl and the Tk Toolkit, Addison, Boston.Google Scholar
  8. 8.
    Welch, B. B. (1999) Practical Programming in Tcl and Tk. 3rd. ed. Prentice Hall, Upper Saddle River, NJ.Google Scholar
  9. 9.
    Schwarzinger, S., Kroon, G. J. A., Foss, T. R., Wright, P. E., and Dyson, H. J. (2000) Random coil chemical shifts in acidic 8 M urea: implementation of random coil shift data in NMRView. J. Biomol. NMR 18, 43–48.PubMedCrossRefGoogle Scholar
  10. 10.
    Felix. (2002) Accelrys, San Diego.Google Scholar
  11. 11.
    Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293.PubMedCrossRefGoogle Scholar
  12. 12.
    VNMR. (2003) Varian, Inc., Palo Alto, CA.Google Scholar
  13. 13.
    XWIN-NMR. (2004) Bruker Biospin GmbH, Rheinstetten, Germany.Google Scholar
  14. 14.
    Chylla, R. A., Volkmann, B. F., and Markley, J. L. (1998) Practical model fitting approaches to the direct extraction of NMR parameters simultaneously from all dimensions of multidimensional NMR spectra. J. Biomol. NMR 12, 277–297.PubMedCrossRefGoogle Scholar
  15. 15.
    Hoch, J. C. and Stern, A. S. (1996) NMR Data Processing, Wiley, New York.Google Scholar
  16. 16.
    Chen, J., De Angelis, A. A., Mandelshtam, V. A., and Shaka, A. J. (2003) Progress on the two-dimensional filter diagonalization method. An efficient doubling scheme for two-dimensional constant-time NMR. J. Magn. Reson. 162, 74–89.PubMedCrossRefGoogle Scholar
  17. 17.
    Koradi, R., Billeter, M., Engeli, M., Güntert, P., and Wüthrich, K. (1998) Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. J. Magn. Reson. 135, 288–297.PubMedCrossRefGoogle Scholar
  18. 18.
    Johnson, B. A., Wilson, E. M., Li, Y., Moller, D. E., Smith, R. G., and Zhou, G. (2000) Ligand-induced stabilization of PPARgamma monitored by NMR spectroscopy: implications for nuclear receptor activation. J. Mol. Biol. 298, 187–194.PubMedCrossRefGoogle Scholar
  19. 19.
    Atreya, H. S., Sahu, S. C., Chary, K. V. R., and Govil, G. (2000) A tracked approach for automated NMR assignments in proteins (TATAPRO). J. Biomol. NMR 17, 125–136.PubMedCrossRefGoogle Scholar
  20. 20.
    Croft, D., Kemmink, J., Neidig, K.-P., and Oschkinat, H. (1997) Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques. J. Biomol. NMR 10, 207–219.PubMedCrossRefGoogle Scholar
  21. 21.
    Hitchens, K. T., Lukin, J. A., Zhan, Y., McCallum, S. A., and Rule, G. S. (2003) MONTE: an automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J. Biomol. NMR 25, 1–9.PubMedCrossRefGoogle Scholar
  22. 22.
    Hyberts, S. G. and Wagner, G. (2003) IBIS—a tool for automated sequential assignment of protein spectra from triple resonance experiments. J. Biomol. NMR 26, 335–344.PubMedCrossRefGoogle Scholar
  23. 23.
    Leutner, M., Gschwind, R. M., Liermann, J., Schwarz, C., Gemmecker, G., and Kessler, H. (1998) Automated backbone assignment of labeled proteins using the threshold accepting algorithm. J. Biomol. NMR 11, 31–43.PubMedCrossRefGoogle Scholar
  24. 24.
    Lukin, J. A., Gove, A. P., Talukdar, S. N., and Ho, C. (1997) Automated probabilistic method for assigning backbone resonances of (13C,15N)-labeled proteins. J. Biomol. NMR 9, 151–166.PubMedCrossRefGoogle Scholar
  25. 25.
    Malmodin, D., Papavoine, C. H. M., and Billeter, M. (2003) Fully automated sequence-specific resonance assignments of hetero-nuclear protein spectra. J. Biomol. NMR 27, 69–79.PubMedCrossRefGoogle Scholar
  26. 26.
    Moseley, H. N. B. and Montelione, G. T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. Biol. 9, 635–642.PubMedCrossRefGoogle Scholar
  27. 27.
    Mumenthaler, C., Güntert, P., Braun, W., and Wüthrich, K. (1997) Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J. Biomol. NMR 10, 351–362.PubMedCrossRefGoogle Scholar
  28. 28.
    Zimmerman, D. E., Kulikowski, C. A., Huang, Y. P., Feng, W. Q., Tashiro, M., Shimotakahara, S., et al. (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J. Mol. Biol. 269, 592–610.PubMedCrossRefGoogle Scholar
  29. 29.
    Friedrichs, M. S., Mueller, L., and Wittekind, M. (1994) An automated procedure for the assignment of protein (HN)-H-1,N-15, C-13(alpha), H-1(alpha), C-13(beta) and H-1(beta) resonances. J. Biomol. NMR 4, 703–726.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2004

Authors and Affiliations

  • Bruce A. Johnson
    • 1
  1. 1.Molecular SystemsMerck Research LabsRahway

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