Question: Which Chemical Compound Interaction Database Is Worth Mentioning?
3
gravatar for Andra Waagmeester
3.1 years ago by
Maastricht, the Netherlands
Andra Waagmeester3.0k wrote:

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?

ADD COMMENTlink modified 3.1 years ago by Larry_Parnell15k • written 3.1 years ago by Andra Waagmeester3.0k
9
gravatar for Lars Juhl Jensen
3.1 years ago by
Copenhagen, Denmark
Lars Juhl Jensen8.5k wrote:

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 :-)

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Lars Juhl Jensen8.5k
8
gravatar for Egon Willighagen
3.1 years ago by
Maastricht
Egon Willighagen4.6k wrote:

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

ADD COMMENTlink modified 3.1 years ago by Lars Juhl Jensen8.5k • written 3.1 years ago by Egon Willighagen4.6k
3
gravatar for Chris Evelo
3.1 years ago by
Chris Evelo8.8k
Maastricht, The Netherlands
Chris Evelo8.8k wrote:

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)
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Chris Evelo8.8k
3
gravatar for Khader Shameer
3.1 years ago by
Rochester, MN
Khader Shameer14k wrote:

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
ADD COMMENTlink written 3.1 years ago by Khader Shameer14k
2
gravatar for Larry_Parnell
3.1 years ago by
Larry_Parnell15k
Boston, MA USA
Larry_Parnell15k wrote:

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

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Larry_Parnell15k
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