Journal of Biomolecular NMR

, Volume 36, Issue 3, pp 147–155 | Cite as

A nomenclature and data model to describe NMR experiments

  • Rasmus H. Fogh
  • Wim F. Vranken
  • Wayne Boucher
  • Tim J. Stevens
  • Ernest D. LaueEmail author


Despite ongoing efforts in organising NMR information, there is no consistent and well-described generic standard for naming NMR experiments. The main reason for the absence of a universal naming system is that the information content of the coherence pathways is difficult to describe in full detail. We propose a system that describes the common and generic elements of the coherence pathways produced by pulse sequences. The system itself is formalised by an ‘NMR experiment protocol’ model, which is described in the Universal Modelling Language (UML) as part of the CCPN data model. Furthermore, normalized experiment names can be derived from this proposed model. We hope this article will stimulate discussion to organise the wealth of NMR experiments, and that by bringing this discussion into the public domain we can improve and expand our proposed system to include as much information and as many NMR experiments as possible.


CCPN data model data standard experiment nomenclature experiment pathway NMR 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.



The authors thank Daniel Nietlispach for very useful discussions to steer the model in the right direction. We are grateful for support from the Biochemistry and Biological Sciences Research Council, UK (Grants 8/B13014 and 8/B20259), and the European Community “Quality of Life and Management of Living Resources” program (Grants QLRI-CT-2001-00015 “TEMBLOR” and QLG2-CT-2000-01313 “NMRQUAL”).

Supplementary material

10858_2006_9076_MOESM1_ESM.pdf (9 kb)
Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.


  1. Aue W.P., Bartholdi E., Ernst R.R. (1976a) J. Chem. Phys. 64:2229–2246CrossRefADSGoogle Scholar
  2. Aue W.P., Karhan J., Ernst R.R. (1976b) J. Chem. Phys. 64:4226–4227CrossRefADSGoogle Scholar
  3. Baran M.C., Moseley H.N., Sahota G., Montelione G.T. (2002) J. Biomol. NMR 24:113–121CrossRefGoogle Scholar
  4. Bax A., Ikura M. (1991) J. Biomol. NMR 1:99–104CrossRefGoogle Scholar
  5. Bax A., Clore G.M., Driscoll P.C., Gronenborn A.M., Ikura M., Kay L.E. (1990a) J. Magn. Reson. 87:620–627Google Scholar
  6. Bax A., Ikura M., Kay L.E., Torchia D.A., Tschudin R. (1990b) J. Magn. Reson. 86:304–318Google Scholar
  7. Bodenhausen G., Ruben D.J. (1980) Chem. Phys. Lett. 69:185–189CrossRefADSGoogle Scholar
  8. Boelens R., Burgering M., Fogh R.H., Kaptein R.E. (1994) J. Biomol. NMR 4:201–213CrossRefGoogle Scholar
  9. Braunschweiler L., Bodenhausen G., Ernst R.R. (1983) Mol. Phys. 48:535–560CrossRefGoogle Scholar
  10. Braunschweiler L., Ernst R.R. (1983) J. Magn. Reson. 53:521–528Google Scholar
  11. Campbell-Burk S.L., Domaille P.J., Starovasnik M.A., Boucher W., Laue E.D. (1992) J. Biomol. NMR 2:639–646CrossRefGoogle Scholar
  12. Clubb R.T., Thanabal V., Wagner G. (1992) J. Biomol. NMR 2:203–210CrossRefGoogle Scholar
  13. Farmer II B.T., Mueller L., Nikonowicz E.P., Pardi A. (1993) J. Am. Chem. Soc. 115:11040–41CrossRefGoogle Scholar
  14. Fogh R., Ionides J., Ulrich E., Boucher W., Vranken W., Linge J.P., Habeck M., Rieping W., Bhat T.N., Westbrook J., Henrick K., Gilliland G., Berman H., Thornton J., Nilges M., Markley J., Laue E. (2002) Nat. Struct. Biol. 9:416–418CrossRefGoogle Scholar
  15. Fogh R.H., Boucher W., Vranken W.F., Pajon A., Stevens T.J., Bhat T.N., Westbrook J., Ionides J.M., Laue E.D. (2005) Bioinformatics 21:1678–1684CrossRefGoogle Scholar
  16. Frenkiel T., Bauer C., Carr M.D., Birdsall B., Feeney J. (1990) J. Magn. Reson. 90:420–425Google Scholar
  17. Grzesiek S., Anglister J., Bax A. (1993) J. Magn. Reson. B 101:114–119CrossRefGoogle Scholar
  18. Grzesiek S., Bax A. (1992) J. Magn. Reson. 96:432–440Google Scholar
  19. Grzesiek S., Bax A. (1993a) J. Biomol. NMR 3:185–204Google Scholar
  20. Grzesiek S., Bax A. (1993b) J. Magn. Reson. B 102:103–106CrossRefGoogle Scholar
  21. Harris R.K., Becker E.D., Cabral de Menezes S.M., Goodfellow R., Granger P. (2002) Concepts Magn. Reson. 14:326–346CrossRefGoogle Scholar
  22. Ikura M., Bax A., Clore G.M., Gronenborn A.M. (1990a) J. Am. Chem. Soc. 112:9020–9022CrossRefGoogle Scholar
  23. Ikura M., Kay L.E., Bax A. (1990b) Biochemistry 29:4659–4667CrossRefGoogle Scholar
  24. Ikura M., Kay L.E., Bax A. (1991) J. Biomol. NMR 1:299–304CrossRefGoogle Scholar
  25. Jeener J., Meier B.H., Bachmann P., Ernst R.R. (1979) J. Chem. Phys. 71:4546–4553CrossRefADSGoogle Scholar
  26. Kay L.E., Ikura M., Bax A. (1990a) J. Am. Chem. Soc. 112:888–889CrossRefGoogle Scholar
  27. Kay L.E., Ikura M., Tschudin R., Bax A. (1990b) J. Magn. Reson. 89:496–514Google Scholar
  28. Kuboniwa H., Grzesiek S., Delaglio F., Bax A. (1994) J. Biomol. NMR 4:871–878CrossRefGoogle Scholar
  29. Logan T.M., Olejniczak E.T., Xu R.X., Fesik S.W. (1993) J. Biomol. NMR 3:225–231CrossRefGoogle Scholar
  30. Lyons B.A., Tashiro M., Cedergren L., Nilsson B., Montelione G.T. (1993) Biochemistry 32:7839–7845CrossRefGoogle Scholar
  31. Marion D., Kay L.E., Sparks S.W., Torchia D.A., Bax A. (1989a) J. Am. Chem. Soc. 111:1515–1517CrossRefGoogle Scholar
  32. Marion D., Driscoll P.C., Kay L.E., Wingfield P.T., Bax A., Gronenborn A.M., Clore G.M. (1989b) Biochemistry 28:6150–6156CrossRefGoogle Scholar
  33. Markley J.L., Bax A., Arata Y., Hilbers C.W., Kaptein R., Sykes B.D., Wright P.E., Wuthrich K. (1998) J. Mol. Biol. 280:933–952CrossRefGoogle Scholar
  34. Montelione G.T., Lyons B.A., Emerson S.D., Tashiro M. (1992) J. Am. Chem. Soc. 114:10974–10975CrossRefGoogle Scholar
  35. Müller L. (1979) J. Am. Chem. Soc. 101:4481–4484CrossRefGoogle Scholar
  36. Norwood T.J., Boyd J., Heritage J.E., Soffe N., Campbell I.D. (1990) J. Magn. Reson. 87:488–501Google Scholar
  37. Olejniczak E.T., Xu R.X., Fesik S.W. (1992) J. Biomol. NMR 2:655–659CrossRefGoogle Scholar
  38. Oschkinat H., Griesinger C., Kraulis P.J., Sorensen O.W., Ernst R.R., Gronenborn A.M., Clore G.M. (1988) Nature 332:374–376CrossRefADSGoogle Scholar
  39. Otting G., Wuthrich K. (1989) J. Magn. Reson. 85:586–594Google Scholar
  40. Palmer 3rd A.G., Fairbrother W.J., Cavanagh J., Wright P.E., Rance M. (1992) J. Biomol. NMR 2:103–108CrossRefGoogle Scholar
  41. Piantini U., Sorensen O.W., Ernst R.R. (1982) J. Am. Chem. Soc. 104:6800–6801CrossRefGoogle Scholar
  42. Powers R., Gronenborn A.M., Marius Clore G., Bax A. (1991) J. Magn. Reson. 94:209–213Google Scholar
  43. Rance M., Sorensen O.W., Bodenhausen G., Wagner G., Ernst R.R., Wuthrich K. (1983) Biochem. Biophys. Res. Commun. 117:479–485CrossRefGoogle Scholar
  44. Sklenar V., Peterson R.D., Rejante M.R., Feigon J. (1993a) J. Biomol. NMR 3:721–727Google Scholar
  45. Sklenar V., Peterson R.D., Rejante M.R.,Wang E., Feigon J. (1993b) J. Am. Chem. Soc. 115:12181–82CrossRefGoogle Scholar
  46. Summers M.F., Bax A. (1986) J. Am. Chem. Soc. 108:2093–2094CrossRefGoogle Scholar
  47. Vranken W.F., Boucher W., Stevens T.J., Fogh R.H., Pajon A., Llinas M., Ulrich E.L., Markley J.L., Ionides J., Laue E.D. (2005) Proteins 59:687–696CrossRefGoogle Scholar
  48. Vuister G.W., Bax A. (1993) J. Am. Chem. Soc. 115:7772–7777CrossRefGoogle Scholar
  49. Vuister G.W., Boelens R., Kaptein R. (1988) J. Magn. Reson. 80:176–185Google Scholar
  50. Wang A.C., Lodi P.J., Qin J., Vuister G.W., Gronenborn A.M., Clore G.M. (1994) J. Magn. Reson. B 105:196–198zbMATHCrossRefGoogle Scholar
  51. Wittekind M., Mueller L. (1993) J. Magn. Reson. B 101:201–205CrossRefGoogle Scholar
  52. Zuiderweg E.R., Fesik S.W. (1989) Biochemistry 28:2387–2391CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Rasmus H. Fogh
    • 1
  • Wim F. Vranken
    • 2
  • Wayne Boucher
    • 1
  • Tim J. Stevens
    • 1
  • Ernest D. Laue
    • 1
    Email author
  1. 1.Department of BiochemistryUniversity of CambridgeCambridgeUK
  2. 2.Macromolecular Structure DatabaseEuropean Bioinformatics Institute, HinxtonCambridgeUK

Personalised recommendations