Chemical databases come in many different types and flavours, and given that we now have UniChem up and running, and it is being actively used by at least some of you, our minds have turned a little to describing these ‘flavours’ and ‘resolutions’. One of the key things a user is interested in is how easy is it to get hold of a compound, since this is usually a key filter applied to actually doing anything with the results of a database search. The cost implications of needing to commission synthesis, or potentially try and develop new synthetic methodology to a compound are substantial, and there is a substantial literature on the computational assessment of synthetic accessibility (q.v.).
- A compound has been previously been synthesized and is readily available from chemical vendors.
- A compound has been previously synthesized but would require resynthesis.
- A compound has not been previously synthesized, but close analogues have and the compound is likely to be readily synthesizable. This class of molecule is often associated with the phrase ‘virtual library’.
- A compound has not been previously synthesized, and effort would be required to think about synthetic access to the compound.
- A compound is theoretically possible with respect to valence rules, but is so unstable that it is unlikely that it ever can be isolated in pure form and then experiments in a biofluid carried out.
Of course, all these classifications are interesting, but you can do a lot more, a lot quicker and cheaper if a compound is in set 1.
- Is this classification useful to apply to the contents of UniChem?
- Is the following classification of the UniChem component databases useful and valid?
- DrugBank, PDBe, IUPHAR, KEGG, ChEBI, Array_Express, NIH_NCC
- ChEMBL, ZINC, eMolecules
- IBM, Patents, SureChem (we don’t currently have GDB in UniChem, but if it was it would be in this set.
See UniChem itself for more details of what is behind these set names.