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.
Similar content being viewed by others
References
Annila, A., Aitio, H., Thulin, E. and Drakenberg, T. (1999) J. Biomol. NMR, 14, 223–230.
Bax, A. and Ottiger, M. (1998) J. Am. Chem. Soc., 120, 12334–12341.
Bax, A. and Tjandra, N. (1997) J. Biomol. NMR, 10, 289–292.
Brennan, R.G. and Matthews, B.W. (1989) J. Biol. Chem., 264, 1903–1906.
Clore, G.M. and Garrett, D.S. (1999) J. Am. Chem. Soc., 121, 9008–9012.
Clore, G.M., Gronenborn, A.M. and Bax, A. (1998) J. Magn. Reson., 133, 216–221.
Clore, G.M., Gronenborn, A.M. and Tjandra, N. (1998) J. Magn. Reson., 131, 159–162.
Cornilescu, G., Marquardt, J.L., Ottiger, M. and Bax, A. (1998) J. Am. Chem. Soc., 120, 6836–6837.
Delaglio, F., Kontaxis, G. and Bax, A. (2000) J. Am. Chem. Soc., 122, 2142–2143.
Fischer, D. and Eisenberg, D. (1999) Curr. Opin. Struct. Biol., 9, 208–211.
Fischer, M.W.F., Losonczi, J.A., Weaver, J.L. and Prestegard, J.H. (1999) Biochemistry, 38, 9013–9022.
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.
Ghose, R. and Prestegard, J.H. (1997) J. Magn. Reson., 128, 138–143.
Harrison, S.C. (1991) Nature, 353, 715–719.
Losonczi, J.A., Andrec, M., Fischer, M.W.F. and Prestegard, J.H. (1999) J. Magn. Reson., 138, 334–342.
Losonczi, J.A. and Prestegard, J.H. (1998) J. Biomol. NMR, 12, 447–451.
Meiler, J., Blomberg, N., Nilges, M. and Griesinger, C. (2000) J. Biomol. NMR, 16, 245–252.
Moult, J. (1999) Curr. Opin. Biotechnol., 10, 583–588.
Ojennus, D.D., Mitton-Fry, R.M. and Wuttke, D.S. (1999) J. Biomol. NMR, 14, 175–179.
Ottiger, M., Zerbe, O., Güntert, P. and Wüthrich, K. (1997) J. Mol. Biol., 272, 64–81.
Patto, C.O. and Saurer, R.T. (1992) Annu. Rev. Biochem., 61, 1053–1095.
Peti, W. and Griesinger, C. (2000), J. Am. Chem. Soc., 122, 3975–3976.
Rost, B. and Sander, C. (1994) Proteins Struct. Funct. Genet., 19, 55–72.
Sali, A. (1998) Nat. Struct. Biol., 5, 1029–1032.
Saupe, A. (1968) Angew. Chem. Int. Ed. Engl., 7, 97–102.
Spera, S. and Bax, A. (1991) J. Am. Chem. Soc., 113, 5490–5492.
Tjandra, N. and Bax, A. (1997) Science, 278, 1111–1113.
Tjandra, N., Grzesiek, S. and Bax, A. (1996) J. Am. Chem. Soc., 118, 6264–6272.
Tolman, J.R., Flanagan, J.M., Kennedy, M.A. and Prestegard, J.H. (1995) Proc. Natl. Acad. Sci. USA, 92, 9279–9283.
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.
Wang, H., Eberstadt, M., Olejniczak, E.T., Meadows, R.P. and Fesik, S.W. (1998) J. Biomol. NMR, 12, 443–446.
Weber, E., Papamokos, E., Bode, W., Huber, R., Kato, I. and Laskowski, M. (1982) J. Mol. Biol., 158, 515–520.
Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995) J. Biomol. NMR, 5, 67–81.
Wishart, D.S. and Sykes, B.D. (1994) J. Biomol. NMR, 4, 171–180.
Wishart, D.S., Sykes, B.D. and Richards, F.M. (1992) Biochemistry, 31, 1647–1651.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Meiler, J., Peti, W. & Griesinger, C. DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts. J Biomol NMR 17, 283–294 (2000). https://doi.org/10.1023/A:1008362931964
Issue Date:
DOI: https://doi.org/10.1023/A:1008362931964