5.5. The use of mmCIF architecture for PDB data management
J. D. Westbrook, H. Yang, Z. Feng and H. M. Berman
Abstract
The Protein Data Bank (PDB) has grown from an archive of seven entries in 1973 to a large and rapidly growing collection of more than 30 000 structures as of May 2005. The PDB now provides a key information resource for the structural biology community. A software framework has been developed that supports automation and scalability, and that can adapt to changes in data content and delivery technology, to permit future development.
The mmCIF data dictionary and an accompanying extended dictionary of local data items provide the core ontology which is the basis for software development. The associated software tools exchange and validate data, create and load databases, translate data formats, and serve application program interfaces. They are made available to the scientific community through an open-source licence.
Links
Figures
A figure in this chapter representing a screenshot of a computer application is reproduced here at full size and in colour.
|
Fig. 5.5.3.3. Example ADIT data-input screen. |
Dictionaries
The following CIF dictionaries are referenced in this chapter:
Software
The following programs are referenced in this chapter:
ADIT
CIFOBJ
- CIFPARSE_OBJ
- FILM
- MMCIF-LOADER
- MMCIF-XML-UTIL
- OpenMMS
- PDB_EXTRACT
- The PDB suite of validation software VAL
Web links
References
Berman, H. M., Henrick, K. & Nakamura, H.
(2003). Announcing the worldwide Protein Data Bank. Nature
Struct. Biol. 10, 980.
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.
![[PubMed]](../graphics/pubmedborder.gif)
![[ChemPort]](../graphics/chemportborder.gif)
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.
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.
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.rcsb.org/pdb/docs/format/pdbguide2.2/part_0.html.
Greer, D. S., Westbrook, J. D. &
Bourne, P. E. (2002). An ontology driven architecture for
derived representations of macromolecular structure.
Bioinformatics, 18, 1280-1281.
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.
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.
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.
Westbrook, J. & Bourne, P. E. (2000).
STAR/mmCIF: an ontology for macromolecular structure.
Bioinformatics, 16, 159-168.