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 > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
