Hi All, I am trying to generate a list of naturally occurring compounds/metabolites of eukaryotes. What I am trying to do is to prune Stitch protein chemical interactions to only the interactions between a protein/enzyme and a naturally occurring ligand. The problem I face is that I am not able to find a comprehensive list of naturally occurring compounds, I retrieved some compounds from KEGG "Compounds with biological roles" but this list is rather small, and I was also playing around with search strategies in PubChem with little success. So has anybody tried to doing this ? any suggestions on a search strategy to retrieve a large list of natural ligands ?
Thank you.
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written
by
Sudeep
1 answer
I think you'll have to concatenate multiple ressources.
Just to name a few:
- Human Metabolome Database
- KNApSAcK database
- Zinc Natural Product catalog. This is just a collection of databases, and I don't think the entries contain the origin of the natural product
You can probably find other database if you just search Google scholar for "natural product database" or "metabolite database".
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