[Zinc-fans] Pubchem vs ZINC

[John J. Irwin]

Hi Huadong

Thanks for your question about ZINC IDs related to PubChem CIDs. Sorry
to take so long to get back to you.

We haven't re-synced with PubChem lately. It is on our list.  When this
is done, they you should be able to simply download a cross reference
table between CID and ZINC ID. For now, I suggest you get the SMILES
from each, canonicalize them, and build fingerprints, e.g. using
E_HASHISY in Cactvs. (xemistry.com). It could be done in as little as a
day, mostly CPU time. There are lots of other ways to do this - this is
just a suggestion.

Hope this helps.

John
UCSF ZINC Team

Huadong Gai wrote:
> I am trying to match compounds in Pubchem with the purchasable
> compounds in ZINC using the SMILES string. I found about 70,000
> compounds and I expect a lot more.
> Are there any differences between the ZINC SMILES and the Openeye
> Canonical or Isomeric SMILES strings in Pubchem? I do not know much
> about SMILES.
> What would be a good way to build a cross reference table between
> COMPOUND_CID in Pubchem and ZINC ID? Is it available anywhere?
>
> Thanks.
>
> H. Gai
>
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