Which Chemical Compound Interaction Database Is Worth Mentioning?

Question

[Andra Waagmeester]

I am trying to collect an extensive list of databases capturing chemical compound interactions with other biological structures. I already have KEGG, HMDB, and WikiPathways

Which resources would you consider to be essential in the context of integrating biological knowledge?

Answer 1

[Lars Juhl Jensen]

The databases that you have listed seem to be focused on metabolites. One obvious database that you should probably include is MetaCyc. If you are also interested in the small-molecule drugs, there is a long list of other databases to include:

• BindingDB
• ChEMBLdb
• CTD
• DrugBank
• GLIDA
• MATADOR
• PDSP Ki
• PharmGKB
• SuperTarget

I probably forgot some more databases that others will point out :-)

Answer 2

[Egon Willighagen]

I would certainly list STITCH and BioMeta (a curated KEGG) too.

Answer 3

[Chris Evelo]

Here are some that Lars missed (great list though!)

• [?]Reactome[?] (or do you consider those to be included in WikiPathways?)
• [?]SMPDB[?] (small molecules pathway database)
• [?]UniPath[?] (manually curated pathway database from UniProt)

Answer 4

[Khader Shameer]

I would like to add two important resources:

• PubChem: Database of chemical structures of small organic molecules and information on their biological activities
• ChEBI: Chemical entities of Biological Interests

Answer 5

[Larry_Parnell]

This review of chemical interactions that pertain to medicinal chemistry seems to be worth a look.