Journal of Biomolecular NMR

, Volume 17, Issue 4, pp 283–294 | Cite as

DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts

  • Jens Meiler
  • Wolfgang Peti
  • Christian Griesinger

Abstract

A program, DipoCoup, is presented that allows to search the protein data bank for proteins which have a three dimensional fold that is at least partially homologous to a protein under investigation. The three dimensional homology search uses secondary structure alignment based on chemical shifts and dipolar couplings or pseudocontact shifts for the three dimensional orientation of secondary structure elements. Moreover, the program offers additional tools for handling and analyzing dipolar couplings.

bioinformatics dipolar couplings postgenomic research protein data base structure elucidation three dimensional homology search 

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References

  1. Annila, A., Aitio, H., Thulin, E. and Drakenberg, T. (1999) J. Biomol. NMR, 14, 223–230.Google Scholar
  2. Bax, A. and Ottiger, M. (1998) J. Am. Chem. Soc., 120, 12334–12341.Google Scholar
  3. Bax, A. and Tjandra, N. (1997) J. Biomol. NMR, 10, 289–292.Google Scholar
  4. Brennan, R.G. and Matthews, B.W. (1989) J. Biol. Chem., 264, 1903–1906.Google Scholar
  5. Clore, G.M. and Garrett, D.S. (1999) J. Am. Chem. Soc., 121, 9008–9012.Google Scholar
  6. Clore, G.M., Gronenborn, A.M. and Bax, A. (1998) J. Magn. Reson., 133, 216–221.Google Scholar
  7. Clore, G.M., Gronenborn, A.M. and Tjandra, N. (1998) J. Magn. Reson., 131, 159–162.Google Scholar
  8. Cornilescu, G., Marquardt, J.L., Ottiger, M. and Bax, A. (1998) J. Am. Chem. Soc., 120, 6836–6837.Google Scholar
  9. Delaglio, F., Kontaxis, G. and Bax, A. (2000) J. Am. Chem. Soc., 122, 2142–2143.Google Scholar
  10. Fischer, D. and Eisenberg, D. (1999) Curr. Opin. Struct. Biol., 9, 208–211.Google Scholar
  11. Fischer, M.W.F., Losonczi, J.A., Weaver, J.L. and Prestegard, J.H. (1999) Biochemistry, 38, 9013–9022.Google Scholar
  12. Friedrich, T., Kröger, B., Bialojan, S., Lemaire, H.G., Höffken, H.W., Reuschenbach, P., Otte, M. and Dodt, J. (1993) J. Biol. Chem., 268, 16216–16220.Google Scholar
  13. Ghose, R. and Prestegard, J.H. (1997) J. Magn. Reson., 128, 138–143.Google Scholar
  14. Harrison, S.C. (1991) Nature, 353, 715–719.Google Scholar
  15. Losonczi, J.A., Andrec, M., Fischer, M.W.F. and Prestegard, J.H. (1999) J. Magn. Reson., 138, 334–342.Google Scholar
  16. Losonczi, J.A. and Prestegard, J.H. (1998) J. Biomol. NMR, 12, 447–451.Google Scholar
  17. Meiler, J., Blomberg, N., Nilges, M. and Griesinger, C. (2000) J. Biomol. NMR, 16, 245–252.Google Scholar
  18. Moult, J. (1999) Curr. Opin. Biotechnol., 10, 583–588.Google Scholar
  19. Ojennus, D.D., Mitton-Fry, R.M. and Wuttke, D.S. (1999) J. Biomol. NMR, 14, 175–179.Google Scholar
  20. Ottiger, M., Zerbe, O., Güntert, P. and Wüthrich, K. (1997) J. Mol. Biol., 272, 64–81.Google Scholar
  21. Patto, C.O. and Saurer, R.T. (1992) Annu. Rev. Biochem., 61, 1053–1095.Google Scholar
  22. Peti, W. and Griesinger, C. (2000), J. Am. Chem. Soc., 122, 3975–3976.Google Scholar
  23. Rost, B. and Sander, C. (1994) Proteins Struct. Funct. Genet., 19, 55–72.Google Scholar
  24. Sali, A. (1998) Nat. Struct. Biol., 5, 1029–1032.Google Scholar
  25. Saupe, A. (1968) Angew. Chem. Int. Ed. Engl., 7, 97–102.Google Scholar
  26. Spera, S. and Bax, A. (1991) J. Am. Chem. Soc., 113, 5490–5492.Google Scholar
  27. Tjandra, N. and Bax, A. (1997) Science, 278, 1111–1113.Google Scholar
  28. Tjandra, N., Grzesiek, S. and Bax, A. (1996) J. Am. Chem. Soc., 118, 6264–6272.Google Scholar
  29. Tolman, J.R., Flanagan, J.M., Kennedy, M.A. and Prestegard, J.H. (1995) Proc. Natl. Acad. Sci. USA, 92, 9279–9283.Google Scholar
  30. van de Locht, A., Lambda, D., Bauer, M., Hubert, R., Friedrich, T., Kroeger, B., Hoffken, W. and Bode, W. (1995) EMBO J., 14, 5149–5155.Google Scholar
  31. Wang, H., Eberstadt, M., Olejniczak, E.T., Meadows, R.P. and Fesik, S.W. (1998) J. Biomol. NMR, 12, 443–446.Google Scholar
  32. Weber, E., Papamokos, E., Bode, W., Huber, R., Kato, I. and Laskowski, M. (1982) J. Mol. Biol., 158, 515–520.Google Scholar
  33. Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995) J. Biomol. NMR, 5, 67–81.Google Scholar
  34. Wishart, D.S. and Sykes, B.D. (1994) J. Biomol. NMR, 4, 171–180.Google Scholar
  35. Wishart, D.S., Sykes, B.D. and Richards, F.M. (1992) Biochemistry, 31, 1647–1651.Google Scholar

Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  • Jens Meiler
    • 1
  • Wolfgang Peti
    • 1
  • Christian Griesinger
    • 1
  1. 1.Institut für Organische ChemieUniversität FrankfurtFrankfurt am Main

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