Re: [ccp4bb] ChEBI and SMILES

Please see https://gitlab.com/-/snippets/2468156 an extension that downloads SDF files > On 7 Oct 2022, at 10:12, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi > > Probably a silly question, but I was wondering how to searc

Re: [ccp4bb] ChEBI and SMILES

On 7 Oct 2022, at 10:12, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:HiProbably 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#

Re: [ccp4bb] ChEBI and SMILES

Hi Gerard API good, web pages bad for this - I’d need to do this 100s of times a day (in spite of AlphaFold, Phyre gets used > 1000 times a day, and I anticipate many users wanting this feature). Using things like SMILES, InChi etc is all to make users’ lives easier - I have to see what’s best

Re: [ccp4bb] ChEBI and SMILES

Hi Harry, On the ChEBI website, if I type a simple SMILES string into the search box (c1c1) 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

Re: [ccp4bb] ChEBI and SMILES

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)

Re: [ccp4bb] ChEBI and SMILES

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 FP

[ccp4bb] ChEBI and SMILES

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 To unsubscribe from the CCP4BB list, click the f