Journal of Biomolecular NMR

, Volume 10, Issue 4, pp 329–336 | Cite as

Automated 1H and 13C chemical shift prediction using the BioMagResBank

  • David S. Wishart
  • M. Scott Watson
  • Robert F. Boyko
  • Brian D. Sykes


A computer program has been developed to accurately and automatically predict the 1H and 13C chemical shifts of unassigned proteins on the basis of sequence homology. The program (called SHIFTY) uses standard sequence alignment techniques to compare the sequence of an unassigned protein against the BioMagResBank – a public database containing sequences and NMR chemical shifts of nearly 200 assigned proteins [Seavey et al. (1991) J. Biomol. NMR, 1, 217–236]. From this initial sequence alignment, the program uses a simple set of rules to directly assign or transfer a complete set of 1H or 13C chemical shifts (from the previously assigned homologues) to the unassigned protein. This ‘homologous assignment’ protocol takes advantage of the simple fact that homologous proteins tend to share both structural similarity and chemical shift similarity. SHIFTY has been extensively tested on more than 25 medium-sized proteins. Under favorable circumstances, this program can predict the 1H or 13C chemical shifts of proteins with an accuracy far exceeding any other method published to date. With the expo- nential growth in the number of assigned proteins appearing in the literature (now at a rate of more than 150 per year), we believe that SHIFTY may have widespread utility in assigning individual members in families of related proteins, an endeavor that accounts for a growing portion of the protein NMR work being done today.

Chemical shift Homology Prediction BioMagResBank 


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  1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) J.Mol.Biol., 215, 403–410.Google Scholar
  2. Bairoch, A. and Apweiler, R. (1996) Nucleic Acids Res., 24, 21–25.Google Scholar
  3. Bartels, C., Billeter, M., Güntert, G. and Wüthrich, K. (1996) J.Biomol. NMR, 7, 207–213.Google Scholar
  4. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.V., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M.J. (1977) J.Mol.Biol., 112, 535–542.Google Scholar
  5. Bryant, S.H. (1996) Proteins Struct.Funct.Genet., 26, 172–185.Google Scholar
  6. Dayhoff, M.O., Barker, W.C. and Hunt, L.T. (1983) Methods Enzymol., 91, 524–545.Google Scholar
  7. De Dios, A.C., Pearson, J.G. and Oldfield, E. (1993) Science, 260, 1491–1495.Google Scholar
  8. George, D.G., Hunt, L.R. and Barker, W.C. (1996) Methods Enzymol., 266, 41–59.Google Scholar
  9. Gronwald, W., Boyko, R.F., Sönnichsen, F.D., Wishart, D.S. and Sykes, B.D. (1997) J.Biomol.NMR, 10, 165–179.Google Scholar
  10. Herranz, J., Gonzalez, C., Rico, M., Nieto, J.L., Santoro, J., Jimenez, M.A., Bruix, M., Neira, J.L. and Blanco, F.J. (1992) Magn.Reson. Chem., 30, 1012–1018.Google Scholar
  11. Herzberg, O. and James, M.N.G. (1988) J.Mol.Biol., 203, 761–771.Google Scholar
  12. Ikura, M., Kay, L.E. and Bax, A. (1990) Biochemistry, 29, 4659–4667.Google Scholar
  13. Needleman, S.B. and Wunsch, C.D. (1970) J.Mol.Biol., 48, 443–453.Google Scholar
  14. Orengo, C.A., Brown, N.P. and Taylor, W.R. (1992) Proteins Struct. Funct.Genet., 14, 139–167.Google Scholar
  15. Ösapay, K. and Case, D.A. (1991) J.Am.Chem.Soc., 113, 9436–9444.Google Scholar
  16. Ösapay, K. and Case, D.A. (1994) J.Biomol.NMR, 4, 215–230.Google Scholar
  17. Perkins, S.J. and Wüthrich, K. (1979) Biochim.Biophys.Acta, 576, 409–422.Google Scholar
  18. Perkins, S.J. and Dwek, R.A. (1980) Biochemistry, 19, 245–255.Google Scholar
  19. Redfield, C. and Robertson, J.P. (1991) In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (Eds., Hoch, J.C., Poulsen, F.M. and Redfield, C.), Plenum, New York, NY, U.S.A., pp. 303–316.Google Scholar
  20. Sali, A., Overington, J.P., Johnson, M.S. and Blundell, R.L. (1990) Trends Biochem.Sci., 15, 235–240.Google Scholar
  21. Seavey, B.R., Farr, E.A., Westler, W.M. and Markley, J.L. (1991) J. Biomol.NMR, 1, 217–236.Google Scholar
  22. Slupsky, C.M., Reinach, F.C., Smillie, L.B. and Sykes, B.D. (1995) Protein Sci., 4, 1279–1290.Google Scholar
  23. Taylor, D.A., Sack, J.S., Maune, J.F. and Beckingham, K. (1991) J. Biol.Chem., 266, 21375–21384.Google Scholar
  24. Williamson, M.P., Asakura, T., Nakamura, E. and Demura, M. (1992) J.Biomol.NMR, 2, 83–98.Google Scholar
  25. Wishart, D.S., Sykes, B.D. and Richards, F.M. (1991) J.Mol.Biol., 222, 311–333.Google Scholar
  26. Wishart, D.S., Boyko, R.F. and Sykes, B.D. (1994) Comput.Appl. Biosci., 10, 121–132.Google Scholar
  27. Wishart, D.S. and Sykes, B.D. (1994) J.Biomol.NMR, 4, 171–180.Google Scholar
  28. Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995a) J.Biomol.NMR, 5, 1–22.Google Scholar
  29. Wishart, D.S., Bigam, C.G., Yao, J., Abildgaard, F., Dyson, H.J., Oldfield, E., Markley, J.L. and Sykes, B.D. (1995b) J.Biomol. NMR, 6, 135–140.Google Scholar

Copyright information

© Kluwer Academic Publishers 1997

Authors and Affiliations

  • David S. Wishart
    • 1
  • M. Scott Watson
    • 1
  • Robert F. Boyko
    • 2
  • Brian D. Sykes
    • 2
  1. 1.Faculty of Pharmacy and Pharmaceutical SciencesUniversity of AlbertaEdmontonCanada
  2. 2.Department of BiochemistryUniversity of AlbertaEdmontonCanada

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