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The Impact of Structural Genomics on the Protein Data Bank

  • Databases and Genome Maps
  • Published:
American Journal of Pharmacogenomics

Abstract

The advent of structural genomics presents new challenges to the archive of biomacromolecular structures — the Protein Data Bank (PDB). As technologies involved in structure determination have advanced, both the number and size of structures available in the PDB have increased rapidly. The structural genomics initiatives are creating a large amount of data that needs to be tracked, archived, and made easily available. The PDB has developed tools to facilitate the rapid deposition of data produced by the structural genomics initiatives and has created databases to track the progress of the work.

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References

  1. Watson HC. The stereochemistry of the protein myoglobin. Prog Stereochem 1969; 4: 299

    CAS  Google Scholar 

  2. Kendrew JC, Bodo G, Dintzis HM, et al. A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 1958; 181: 662–6

    Article  PubMed  CAS  Google Scholar 

  3. Bolton W, Perutz MF. Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Ångstrom units resolution. Nature 1970; 228(271): 551–2

    Article  PubMed  CAS  Google Scholar 

  4. Perutz MF, Rossmann MG, Cullis AF, et al. Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5 Å resolution. Nature 1960; 185: 416–22

    Article  PubMed  CAS  Google Scholar 

  5. Bernstein FC, Koetzle TF, Williams GJB, et al. Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977; 112: 535–42

    Article  PubMed  CAS  Google Scholar 

  6. Berman HM, Bourne PE, Westbrook J. The protein data bank: a case study in management of community data. Curr Proteomics 2004; 1: 49–57

    Article  CAS  Google Scholar 

  7. NCBI entrez genome [online]. Available from URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?.db=Genome [Accessed 2004 Apr 8]

  8. Nat Struct Biol. Structural genomics. Nat Struct Biol 2000; 7Suppl. Issue: 927–94

    Google Scholar 

  9. Protein Structure Initiative: better tools and better knowledge for structural genomics [online]. Available from URL: http://www.nigms.nih.gov/psi/ [Accessed 2004 Apr 8]

  10. Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res 2000; 28(1): 235–42

    Article  PubMed  CAS  Google Scholar 

  11. RCSB Protein Data Bank [online]. Available from URL: http://www.pdb.org/ [Accessed 2004 Apr 8]

  12. Westbrook J, Feng Z, Burkhardt K, et al. Validation of protein structures for the Protein Data Bank. Methods Enzymol 2003 374: 370–85

    Article  PubMed  CAS  Google Scholar 

  13. Bourne PE, Berman HM, Watenpaugh K, et al. The macromolecular crystallographic information file (mmCIF). Methods Enzymol 1997; 277: 571–90

    Article  PubMed  CAS  Google Scholar 

  14. mmCIF resources: about the macromolecular Crystallographic Information File format [online]. Available from URL: http://deposit.pdb.org/mmcif/ [Accessed 2004 Apr 8]

  15. Conte L, Bart A, Hubbard T, et al. SCOP: a structural classification of proteins database. Nucleic Acids Res 2000; 28(1): 257–9

    Article  PubMed  Google Scholar 

  16. Conte LL, Brenner SE, Hubbard TJ, et al. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 2002; 30(1): 264–7

    Article  PubMed  Google Scholar 

  17. Orengo CA, Michie AD, Jones S, et al. CATH: a hierarchic classification of protein domain structures. Structure 1997; 5: 1093–108

    Article  PubMed  CAS  Google Scholar 

  18. Pearl FMG, Lee D, Bray JE, et al. The CATH extended protein-family database: providing structural annotations for genome sequences. Protein Sci 2002; 11: 233–44

    Article  PubMed  CAS  Google Scholar 

  19. Mycobacterium tuberculosis structural genomics consortium [online]. Available from URL: http://www.doe-mbi.ucla.edu/TB/ [Accessed 2004 Apr 8]

  20. Berkeley Structural Genomics Center [online]. Available from URL: http://www.strgen.org/ [Accessed 2004 Apr 8]

  21. Hendrickson WA. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 1991; 254: 51–8

    Article  PubMed  CAS  Google Scholar 

  22. PDB software tools [online]. Available from URL: http://deposit.pdb.org/software/ [Accessed 2004 Apr 8]

  23. TargetDB: target search for structural genomics [online]. Available from URL: http://targetdb.pdb.org/ [Accessed 2004 Apr 8]

  24. Task Force on Target Tracking [online]. Task Force Reports from the Second International Structural Genomics Meeting; 2001 Apr 4–6; Airlie (VA). 2001. Available from URL: http://www.nigms.nih.gov/news/meetings/airlie.html [Accessed 2004 Apr 8]

  25. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 1988; 24: 2444–8

    Article  Google Scholar 

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Acknowledgements

The RCSB Protein Data Bank is managed by three members of the Research Collaboratory for Structural Bioinformatics — Rutgers University, SDSC/UCSD, and CARB/NIST — and is funded by the National Science Foundation, the Department of Energy, and the National Institutes of Health.

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Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey, 08854, USA

    Helen M. Berman & John D. Westbrook

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  1. Helen M. Berman
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  2. John D. Westbrook
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Correspondence to Helen M. Berman.

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Berman, H.M., Westbrook, J.D. The Impact of Structural Genomics on the Protein Data Bank. Am J Pharmacogenomics 4, 247–252 (2004). https://doi.org/10.2165/00129785-200404040-00004

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  • DOI: https://doi.org/10.2165/00129785-200404040-00004

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