Journal of Biomolecular NMR

, Volume 24, Issue 2, pp 113–121 | Cite as

SPINS: Standardized ProteIn NMR Storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra

  • Michael C. Baran
  • Hunter N.B. Moseley
  • Gurmukh Sahota
  • Gaetano T. Montelione

Abstract

Modern protein NMR spectroscopy laboratories have a rapidly growing need for an easily queried local archival system of raw experimental NMR datasets. SPINS (Standardized ProteIn Nmr Storage) is an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and dissemination of results to the public domain by automatic preparation of the header files required for submission of data to the BioMagResBank (BMRB). The current version of SPINS coordinates the process from data collection to BMRB deposition of raw NMR data by standardizing and integrating the storage and retrieval of these data in a local laboratory file system. Additional facilities include a data mining query tool, graphical database administration tools, and a NMRStar v2.1.1 file generator. SPINS also includes a user-friendly internet-based graphical user interface, which is optionally integrated with Varian VNMR NMR data collection software. This paper provides an overview of the data model underlying the SPINS database system, a description of its implementation in Oracle, and an outline of future plans for the SPINS project.

integrated analysis process NMR spectra archive Oracle database structural genomics 

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References

  1. Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shndyalov I. and Bourne, P. (2000) Nucl. Acids Res., 28, 235–242.CrossRefGoogle Scholar
  2. Bertone, P., Kluger, Y., Lan, Y., Zheng, D., Christendat, D., Yee, A., Edwards, A.M., Arrowsmith, C.H., Montelione, G.T. and Gerstein, M. (2001) Nucl. Acids Res., 29, 2884–2898.CrossRefGoogle Scholar
  3. Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and Warren, G.L. (1998) Acta Cryst., D54, 905–921.CrossRefGoogle Scholar
  4. Delaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer, J. and Bax, A. (1995) J. Biomol. NMR,6, 277–293.CrossRefGoogle Scholar
  5. Goddard, T.D. and Kneller, D.G. (2000) SPARKY 3, University of California, San Francisco, CA.Google Scholar
  6. Güntert, P., Mumenthaler, C. and Wüthrich, K. (1997) J. Mol. Biol., 273, 283–298CrossRefGoogle Scholar
  7. Heinemann, U. (2000) Nat.Struct. Biol., 7, 940–942.CrossRefGoogle Scholar
  8. Huang, Y.J. (2001) Automated Determination of Protein Structures from NMR Data byIterative Analysis of Self-Consistent Contact Patterns, Ph.D. Thesis, Rutgers, The State University of New Jersey, Piscataway, NJ.Google Scholar
  9. Monleón, D., Colson, K., Moseley, H.N.B., Anklin, C., Oswald, R., Szyperski, T.A. and Montelione, G.T. (2002) J.Struct. Funct. Genomics, 2, 93–101.CrossRefGoogle Scholar
  10. Montelione, G.T., Zheng, D., Huang, Y.J., Gunsalus, K.C. and Szyperski, T.(2000) Nat. Struct. Biol., 7, 982–985.CrossRefGoogle Scholar
  11. Moseley, H.N.B., Monleon, D. and Montelione, G.T. (2001) Meth.Enzymol., 339, 91–108.CrossRefGoogle Scholar
  12. Seavey, B.R., Farr, E.A., Westler, W.M. and Markley, J. (1991) J. Biomol. NMR, 1,217–236.CrossRefGoogle Scholar
  13. Terwilliger, T.C. (2000) Nat. Struct. Biol., 7, 935–939.CrossRefGoogle Scholar
  14. Yokoyama, S., Hirota, H., Kigawa, T., Yabuki, T., Shirouzu, M., Terada, T., Ito, Y., Matsuo, Y., Kuroda, Y., Nishimura, Y., Kyogoku, Y., Miki, K., Masui, R. and Kuramitsu, S. (2000) Nat. Struct. Biol., 7, 943–945.CrossRefGoogle Scholar
  15. Zimmerman, D.E., Kulikowski, C.A., Huang, Y., Feng, W., Tashiro, M., Shimotakahara, S., Chien, S.Y., Powers, R. and Montelione, G.T. (1997) J. Mol. Biol., 269, 592–610.CrossRefGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Michael C. Baran
    • 1
  • Hunter N.B. Moseley
    • 1
  • Gurmukh Sahota
    • 1
  • Gaetano T. Montelione
    • 1
  1. 1.Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and BiochemistryRutgers UniversityPiscatawayU.S.A
  2. 2.Department of Biochemistry and Molecular BiologyRobert Wood Johnson Medical SchoolPiscatawayU.S.A.

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