END: Enzyme Nomenclature Database
Sinead Boyce1, Avanthi Mummaneni2, Bhavani Akunuri2, Andrej Bugrim3, Andrew McDonald1, Jakub Slomczynski3, Francis Frabizio3, Waheeda Sulaman2, William B. Wise2, Keith Tipton1, and Toni Kazic2
1Trinity College, Dublin, Ireland 2University of Missouri, Columbia 3Washington University
END is a database built from the Enzyme Nomenclature. The Nomenclature is maintained by the IUBMB/IUPAC Joint Committees on Biochemical Nomenclature (JCBN). We are placing END version 2.0 in the public domain and invite you to use it freely. We ask only that you follow good scholarly practice and credit our work, and preserve the accession numbers for each datum.
Several aspects of version 2.0 of END are worth noting:
- all accession numbers are permanently assigned;
- all minor datatypes (e.g. glossary and reaction diagram figures), have been incorporated or referenced;
- references to other databases are current, and distinguish between search strings and accession numbers;
- cross-references to PDB and other databases have been corrected;
- simple histories of entries are presented;
- and a number of names for small molecules have been changed throughout the data. These include resolution of some internal synonyms (more than one name for the same compound in the database); making syntactic inconsistencies in the names consistent (for example, nucleotide sugars now all have a dash between the nucleotide and the sugar moieties); making the names of nicotinamide cofactors consistent with current recommendations in all fields except synonyms for enzyme names which are not systematic names; and correction of miscellaneous errors, including typographical ones. Many of these synonyms, along with many others we have uncovered, are presented in BND.
We have been very conservative about changing names, and many more corrections await approval by the JCBN. You can read about the proposed changes and current questions here.
There is much more work to be done. All reactions should be expressed by equations; data expressed or implied in the comments must be made explicit; phylogenetic, tissue, and isoenzyme information must be added; information on other reactions, substrates, inhibitors, and their kinetics and thermodynamics should be included. A similar situation exists with respect to small molecule nomenclature: we have identified the ambiguous names in the nomenclature, but tracking down exactly which molecule (or set of molecules) is (are) meant in a given entry will take time. Complex histories are being interpreted and resolved by Dr. Sinead Boyce.
You may download a tar file containing all the data. You will find the comments at the beginning of each file useful in understanding its syntax and semantics.
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