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Conceptual Data Modeling

The IUPAC recommendations for biochemical nomenclature (1-3) imply a Conceptual Data Model (CDM) for protein structure. The following entity-relationship diagram describes the implied conceptual data model and is easily implemented in commercial database programs such as Microsoft Access and MySQL.

As a demonstration of the validity and usefulness of the proposed CDM we provide an Access implementation for download which has been populated with experimental data from the Protein Data Bank. Analysis of the CDM is given in: Fox-Erlich, S., Martyn, T.O., Ellis, H.J.C., & Gryk, M.R. Delineation and analysis of the conceptual data model implied by the "IUPAC Recommendations for Biochemical Nomenclature." Protein Sci 2004 13, 2559-2563. PUBMED: 15295113

  1. IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. Tentative rules (1969). Biochemistry 1970 9, 3471-9. PUBMED: 5509841
  2. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature and symbolism for amino acids and peptides. Recommendations 1983. Eur J Biochem. 1984 138, 9-37. PUBMED: 6692818
  3. Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, & Wuthrich K. Recommendations for the presentation of NMR structures of proteins and nucleic acids. J Mol Biol. 1998 280, 933-52. PUBMED: 9671561