The use of mmCIF architecture for PDB data management

Westbrook, J. D.; Yang, H.; Feng, Z.; Berman, H. M.

doi:10.1107/97809553602060000755

International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G. ch. 5.5, pp. 539-543
https://doi.org/10.1107/97809553602060000755

Chapter 5.5. The use of mmCIF architecture for PDB data management

J. D. Westbrook,^a ^* H. Yang,^a Z. Feng^a and H. M. Berman^a

^a Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
Correspondence e-mail: [email protected]

References

Berman, H. M., Henrick, K. & Nakamura, H. (2003). Announcing the worldwide Protein Data Bank. Nature Struct. Biol. 10, 980.Google Scholar

Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235–242.Google Scholar

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542. Google Scholar

Bourne, P. E., Berman, H. M., McMahon, B., Watenpaugh, K. D., Westbrook, J. D. & Fitzgerald, P. M. D. (1997). Macromolecular Crystallographic Information File. Methods Enzymol. 277, 571–590.Google Scholar

Callaway, J., Cummings, M., Deroski, B., Esposito, P., Forman, A., Langdon, P., Libeson, M., McCarthy, J., Sikora, J., Xue, D., Abola, E., Bernstein, F., Manning, N., Shea, R., Stampf, D. & Sussman, J. (1996). Protein Data Bank contents guide: Atomic coordinate entry format description. Brookhaven National Laboratory, New York, USA. Available from http://www.wwpdb.org/documentation/PDB_format_1996.pdf .Google Scholar

Greer, D. S., Westbrook, J. D. & Bourne, P. E. (2002). An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics, 18, 1280–1281.Google Scholar

Kuller, A., Fleri, W., Bluhm, W. F., Smith, J. L., Westbrook, J. & Bourne, P. E. (2002). A biologist's guide to synchrotron facilities: the BioSync web resource. Trends Biochem. Sci. 27, 213–215.Google Scholar

Schirripa, S. & Westbrook, J. D. (1996). CIFOBJ. A class library of mmCIF access tools. Reference guide. http://sw-tools.pdb.org/apps/CIFOBJ/cifobj/index.html .Google Scholar

Tosic, O. & Westbrook, J. D. (2000). CIFParse. A library of access tools for mmCIF. Reference guide. http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/cifparse/index.html .Google Scholar

Westbrook, J. & Bourne, P. E. (2000). STAR/mmCIF: an ontology for macromolecular structure. Bioinformatics, 16, 159–168.Google Scholar