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Which Chemical Compound Interaction Database Is Worth Mentioning?

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?

chemoinformatics interaction database
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updated by Larry_Parnell Larry_Parnell • written by Andra Waagmeester Andra Waagmeester

5 answers

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:

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

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written by Lars Juhl Jensen Lars Juhl Jensen

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

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updated by Lars Juhl Jensen Lars Juhl Jensen • written by Egon Willighagen Egon Willighagen

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)
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written by Chris Evelo Chris Evelo

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
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updated by Ram Ram • written by Khader Shameer Khader Shameer

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

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written by Larry_Parnell Larry_Parnell

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