The Brookhaven Protein Data Bank was once a pioneering database, but its organization of structural data is now outdated and in need of an upgrade.
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References
Editorial. Nature 440, 383 (2006).
Hey, T. & Trefethon, A. in Grid Computing—Making the Global Infrastructure a Reality (eds., Berman, F., Fox, G.C. & Hey, A.J.G.) 809–824, (John Wiley & Sons, Inc., New York, USA).
Bourne, P., Berman, H.M., Watenpaugh, K., Westbrook, J. & Fitzgerald, P.M.D. Meth. Enzymol. 277, 571–590 (1997).
Deshpande, N. et al. Nucleic Acids Res. 33, D233–D237 (2005).
Rosse, C. & Mejino, J.L.V. J. Biomed. Inform. 36, 478–500 (2003).
Whetzel, P.L. et al. OMICS 10, 199–204 (2006).
Westbrook, J.D. & Bourne, P.E. Bioinformatics 16, 159–168 (2000).
http://ontology.buffalo.edu/ (last visited March 2007).
http://www.rcsb.org/pdbschema/index.html (last visited March 2007).
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl (last visited March 2007)
http://deposit.pdb.org/public-component-erf.cif (last visited March 2007).
Codd, E.F. Commun. ACM 13, 377–387 (1970).
http://www.iucr.org/iucr-top/cif/standard/cifstd8.html (last visited March 2007).
http://pdbbeta.rcsb.org/pdbschema/ (last visited March 2006).
http://www.ciobriefings.com/whitepapers/StarSchema.asp (last visited March 2007).
Soldatova, L. & King, R.D. J. Royal Society Interface 3/11: 795–803 (2006).
http://suo.ieee.org/ (last visited March 2007).
Acknowledgements
We would like to thank Alexei Adzhubei. The work was funded by the Framework 6 IQ project (516169) and Biotechnology and Biological Sciences Research Council (Project 2/BEP17028).
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Schierz, A., Soldatova, L. & King, R. Overhauling the PDB. Nat Biotechnol 25, 437–442 (2007). https://doi.org/10.1038/nbt0407-437
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DOI: https://doi.org/10.1038/nbt0407-437
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