PDBx/mmCIF References

  • J. D.Westbrook, J. Y.Young, C. Shao, Z. Feng, V. Guranovic, C. L. Lawson, B. Vallat, P. D.Adams, J. M. Berrisford, G. Bricogne, K. Diederichs, R. P.Joosten, P. Keller, N. W. Moriarty, O. V.Sobolev, S. Velankar, C. Vonrhein, D. G. Waterman, G. Kurisu, H. M. Berman, S. K. Burley, E. Peisach. PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology, (2022), Journal of Molecular Biology in press
  • Chapter 10 The PDB format, mmCIF formats, and other data formats. In Structural Bioinformatics, J. D. Westbrook, P. M. D. Fitzgerald. (2009). Second Edition (P. E. Bourne & J. Gu, eds.), pp. 271-291. John Wiley & Sons, Inc., Hoboken, New Jersey.
  • Chapter 3.6. Classification and use of macromolecular data. (PDF) in International Tables for Crystallography G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. 2005, Springer: Dordrecht, The Netherlands. p. 144-198.
  • Chapter 3.6.2 The Protein Data Bank exchange dictionary (PDF) Westbrook J, Henrick K, Ulrich EL, Berman HM. (2005). in International Tables for Crystallography G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors, Springer: Dordrecht, The Netherlands. p. 195-198.
  • Chapter 4.5. The Macromolecular dictionary (mmCIF) Fitzgerald PMD, Westbrook JD, Bourne PE, McMahon B, Watenpaugh KD, Berman HM. (2005). in International Tables for Crystallography, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 295-443.
  • Chapter 2.6 Specification of a relational Dictionary Definition Language (DDL2). J. D. Westbrook, H. M. Berman, S. R. Hall. (2005). in International Tables for Crystallography (S. R. Hall & B. McMahon, eds.), Vol. G. Definition and exchange of crystallographic data, pp. 61-72. Springer, Dordrecht, The Netherlands.
  • Chapter 5.5 The use of mmCIF architecture for PDB data management. Westbrook J, Yang H, Feng Z, Berman HM. (2005). in International Tables for Crystallography (S. R. Hall & B. McMahon, eds.), Vol. G. Definition and exchange of crystallographic data, pp. 539-543. Springer, Dordrecht, The Netherlands.
  • PDBML: the representation of archival macromolecular structure data in XML. John Wesbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick and Helen M. Berman, Bioinformatics, 21(7), 988-992, 2005.
  • STAR/mmCIF: An Extensive Ontology for Macromolecular Structure and Beyond (PDF) Westbrook J, Bourne PE. Bioinformatics (2000) 16(2), 159-168.
  • J. D. Westbrook, S.-H. Hsieh, P. M. D. Fitzgerald. CIF Applications. VI. CIFLIB: an application-program interface to CIF dictionaries and data files. J. Appl. Cryst. (1997) 30, 79-83.
  • The Macromolecular Crystallographic Information File (mmCIF) Meth. Enzymol. (1997) 277, 571-590.
  • How the Nucleic Acid Database Uses CIF. H. M. Berman and J. D. Westbrook, in Proceedings of the First Macromolecular CIF Tools Workshop, P. E. Bourne, ed. (1993) National Science Foundation, Tarrytown, New York, p. 65.
  • The STAR File: a New Format for Electronic Data Transfer and Archiving, S. R. Hall, J. Chem. Inf. Comp. Sci. (1991) 31, 326-333.
  • The Crystallographic Information file (CIF): a New Standard Archive File for Crystallography, S. R. Hall, A. H. Allen, and I. D. Brown, Acta Cryst. (1991) A47, 655-685.