Hi Harry,
On the ChEBI website, if I type a simple SMILES string into the search box
(c1ccccc1) it takes me to the corresponding entity page. I don't know if they
have an API that supports this but I'm sure the friendly folks of the ChEBI
helpdesk (https://www.ebi.ac.uk/chebi/emailChebiForward.do) can tell you.
Another resource that may be of use in this context is UniChem
(https://www.ebi.ac.uk/unichem/). You provide an InChI (not SMILES
unfortunately) and it will then return a list of the identifiers of the
compound in bunch of resources (incl. ChEMBL, ChEBI, PDB, PubChem, Zinc, etc.)
- if they exist in that resource of course. (It offers an API so is good for
programmatic access - https://www.ebi.ac.uk/unichem/api/docs )
You can also provide a compound ID from any of those resources to find out
what it is called in the other resources (if it exists there), e.g.
https://www.ebi.ac.uk/unichem/compoundsources?type=sourceID&compound=BNZ&sourceID=3
searches for the compound we know as BNZ in the PDB.
Hope this helps,
--Gerard
On Fri, 7 Oct 2022, Harry Powell wrote:
Hi Jeet
This is very useful - many thanks.
I was hoping there might be some kind of API for searching the ChEBI database
online, but there we go…
It looks like downloading the ChEBI database is the first step here, since many
entries appear to have SMILES information.
But (important to note) ChEBI ≠ ChEMBL, although there is an overlap (a
considerable ione…).
Harry
On 7 Oct 2022, at 10:29, jeet balraj <jeetendra...@gmail.com> wrote:
Hi Harry
To search the ligand of interest in the ChEMBL database, you can follow these
simple steps:
1. download the ChEMBL database and extract all its SMILES.
2. calculate the MorganFingerprint of each of the SMILES in the database.
3. calculate the MorganFingerprint of your ligand.
4. use the FPSim2 package from ChEMBL for the Tanimoto similarity search.
you can use RDKit to calculate the morgan fingerprints of each SMILES string.
Note: you have to first convert each SMILES in the database to canonical form.
I hope this helps.
Thanks
Jitendra Kuldeep
Postdoc researcher
Machine learning and precision oncology group
Cancer research center of marseille, INSERM
France 13009
On Fri, Oct 7, 2022 at 11:13 AM Harry Powell
<0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
Hi
Probably a silly question, but I was wondering how to search for a ligand in
ChEBI with a SMILES string? It’s not immediately obvious to my Friday-morning
mind ...
Harry
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Best wishes,
--Gerard
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Gerard J. Kleywegt
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