Skip to main content
SpringerLink
Log in

A nomenclature and data model to describe NMR experiments

  • Article
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Aue W.P., Bartholdi E., Ernst R.R. (1976a) J. Chem. Phys. 64:2229–2246

    Article  ADS  Google Scholar 

  • Aue W.P., Karhan J., Ernst R.R. (1976b) J. Chem. Phys. 64:4226–4227

    Article  ADS  Google Scholar 

  • Baran M.C., Moseley H.N., Sahota G., Montelione G.T. (2002) J. Biomol. NMR 24:113–121

    Article  Google Scholar 

  • Bax A., Ikura M. (1991) J. Biomol. NMR 1:99–104

    Article  Google Scholar 

  • Bax A., Clore G.M., Driscoll P.C., Gronenborn A.M., Ikura M., Kay L.E. (1990a) J. Magn. Reson. 87:620–627

    Google Scholar 

  • Bax A., Ikura M., Kay L.E., Torchia D.A., Tschudin R. (1990b) J. Magn. Reson. 86:304–318

    Google Scholar 

  • Bodenhausen G., Ruben D.J. (1980) Chem. Phys. Lett. 69:185–189

    Article  ADS  Google Scholar 

  • Boelens R., Burgering M., Fogh R.H., Kaptein R.E. (1994) J. Biomol. NMR 4:201–213

    Article  Google Scholar 

  • Braunschweiler L., Bodenhausen G., Ernst R.R. (1983) Mol. Phys. 48:535–560

    Article  Google Scholar 

  • Braunschweiler L., Ernst R.R. (1983) J. Magn. Reson. 53:521–528

    Google Scholar 

  • Campbell-Burk S.L., Domaille P.J., Starovasnik M.A., Boucher W., Laue E.D. (1992) J. Biomol. NMR 2:639–646

    Article  Google Scholar 

  • Clubb R.T., Thanabal V., Wagner G. (1992) J. Biomol. NMR 2:203–210

    Article  Google Scholar 

  • Farmer II B.T., Mueller L., Nikonowicz E.P., Pardi A. (1993) J. Am. Chem. Soc. 115:11040–41

    Article  Google Scholar 

  • 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. 9:416–418

    Article  Google Scholar 

  • 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 21:1678–1684

    Article  Google Scholar 

  • Frenkiel T., Bauer C., Carr M.D., Birdsall B., Feeney J. (1990) J. Magn. Reson. 90:420–425

    Google Scholar 

  • Grzesiek S., Anglister J., Bax A. (1993) J. Magn. Reson. B 101:114–119

    Article  Google Scholar 

  • Grzesiek S., Bax A. (1992) J. Magn. Reson. 96:432–440

    Google Scholar 

  • Grzesiek S., Bax A. (1993a) J. Biomol. NMR 3:185–204

    Google Scholar 

  • Grzesiek S., Bax A. (1993b) J. Magn. Reson. B 102:103–106

    Article  Google Scholar 

  • Harris R.K., Becker E.D., Cabral de Menezes S.M., Goodfellow R., Granger P. (2002) Concepts Magn. Reson. 14:326–346

    Article  Google Scholar 

  • Ikura M., Bax A., Clore G.M., Gronenborn A.M. (1990a) J. Am. Chem. Soc. 112:9020–9022

    Article  Google Scholar 

  • Ikura M., Kay L.E., Bax A. (1990b) Biochemistry 29:4659–4667

    Article  Google Scholar 

  • Ikura M., Kay L.E., Bax A. (1991) J. Biomol. NMR 1:299–304

    Article  Google Scholar 

  • Jeener J., Meier B.H., Bachmann P., Ernst R.R. (1979) J. Chem. Phys. 71:4546–4553

    Article  ADS  Google Scholar 

  • Kay L.E., Ikura M., Bax A. (1990a) J. Am. Chem. Soc. 112:888–889

    Article  Google Scholar 

  • Kay L.E., Ikura M., Tschudin R., Bax A. (1990b) J. Magn. Reson. 89:496–514

    Google Scholar 

  • Kuboniwa H., Grzesiek S., Delaglio F., Bax A. (1994) J. Biomol. NMR 4:871–878

    Article  Google Scholar 

  • Logan T.M., Olejniczak E.T., Xu R.X., Fesik S.W. (1993) J. Biomol. NMR 3:225–231

    Article  Google Scholar 

  • Lyons B.A., Tashiro M., Cedergren L., Nilsson B., Montelione G.T. (1993) Biochemistry 32:7839–7845

    Article  Google Scholar 

  • Marion D., Kay L.E., Sparks S.W., Torchia D.A., Bax A. (1989a) J. Am. Chem. Soc. 111:1515–1517

    Article  Google Scholar 

  • Marion D., Driscoll P.C., Kay L.E., Wingfield P.T., Bax A., Gronenborn A.M., Clore G.M. (1989b) Biochemistry 28:6150–6156

    Article  Google Scholar 

  • Markley J.L., Bax A., Arata Y., Hilbers C.W., Kaptein R., Sykes B.D., Wright P.E., Wuthrich K. (1998) J. Mol. Biol. 280:933–952

    Article  Google Scholar 

  • Montelione G.T., Lyons B.A., Emerson S.D., Tashiro M. (1992) J. Am. Chem. Soc. 114:10974–10975

    Article  Google Scholar 

  • Müller L. (1979) J. Am. Chem. Soc. 101:4481–4484

    Article  Google Scholar 

  • Norwood T.J., Boyd J., Heritage J.E., Soffe N., Campbell I.D. (1990) J. Magn. Reson. 87:488–501

    Google Scholar 

  • Olejniczak E.T., Xu R.X., Fesik S.W. (1992) J. Biomol. NMR 2:655–659

    Article  Google Scholar 

  • Oschkinat H., Griesinger C., Kraulis P.J., Sorensen O.W., Ernst R.R., Gronenborn A.M., Clore G.M. (1988) Nature 332:374–376

    Article  ADS  Google Scholar 

  • Otting G., Wuthrich K. (1989) J. Magn. Reson. 85:586–594

    Google Scholar 

  • Palmer 3rd A.G., Fairbrother W.J., Cavanagh J., Wright P.E., Rance M. (1992) J. Biomol. NMR 2:103–108

    Article  Google Scholar 

  • Piantini U., Sorensen O.W., Ernst R.R. (1982) J. Am. Chem. Soc. 104:6800–6801

    Article  Google Scholar 

  • Powers R., Gronenborn A.M., Marius Clore G., Bax A. (1991) J. Magn. Reson. 94:209–213

    Google Scholar 

  • Rance M., Sorensen O.W., Bodenhausen G., Wagner G., Ernst R.R., Wuthrich K. (1983) Biochem. Biophys. Res. Commun. 117:479–485

    Article  Google Scholar 

  • Sklenar V., Peterson R.D., Rejante M.R., Feigon J. (1993a) J. Biomol. NMR 3:721–727

    Google Scholar 

  • Sklenar V., Peterson R.D., Rejante M.R.,Wang E., Feigon J. (1993b) J. Am. Chem. Soc. 115:12181–82

    Article  Google Scholar 

  • Summers M.F., Bax A. (1986) J. Am. Chem. Soc. 108:2093–2094

    Article  Google Scholar 

  • 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 59:687–696

    Article  Google Scholar 

  • Vuister G.W., Bax A. (1993) J. Am. Chem. Soc. 115:7772–7777

    Article  Google Scholar 

  • Vuister G.W., Boelens R., Kaptein R. (1988) J. Magn. Reson. 80:176–185

    Google Scholar 

  • Wang A.C., Lodi P.J., Qin J., Vuister G.W., Gronenborn A.M., Clore G.M. (1994) J. Magn. Reson. B 105:196–198

    Article  MATH  Google Scholar 

  • Wittekind M., Mueller L. (1993) J. Magn. Reson. B 101:201–205

    Article  Google Scholar 

  • Zuiderweg E.R., Fesik S.W. (1989) Biochemistry 28:2387–2391

    Article  Google Scholar 

Download references

Acknowledgements

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”).

Author information

Authors and Affiliations

  1. Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK

    Rasmus H. Fogh, Wayne Boucher, Tim J. Stevens & Ernest D. Laue

  2. Macromolecular Structure Database, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK

    Wim F. Vranken

Authors
  1. Rasmus H. Fogh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wim F. Vranken
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wayne Boucher
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tim J. Stevens
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ernest D. Laue
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ernest D. Laue.

Additional information

Joint first authors

Electronic supplementary material

10858_2006_9076_MOESM1_ESM.pdf

Electronic supplementary material Supplementary material is available in the online version of this article at http://www.dx.doi.org/10.1007/s10858-006-9076-z and is accessible for authorized users.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fogh, R.H., Vranken, W.F., Boucher, W. et al. A nomenclature and data model to describe NMR experiments. J Biomol NMR 36, 147–155 (2006). https://doi.org/10.1007/s10858-006-9076-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-006-9076-z

Keywords

Search

Navigation