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. Many thanks for this - your colleagues at EBI have already been very helpful (but chose to reply off-list) - I’ll prepare a digest RSN… Harry > On 7 Oct 2022, at 15:15, Gerard Kleywegt <ger...@xray.bmc.uu.se> wrote: > > 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 >>> ######################################################################## >>> >>> 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/ >> > > > Best wishes, > > --Gerard > > ****************************************************************** > Gerard J. Kleywegt > > http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se > ****************************************************************** > The opinions in this message are fictional. Any similarity > to actual opinions, living or dead, is purely coincidental. > ****************************************************************** > Little known gastromathematical curiosity: let "z" be the > radius and "a" the thickness of a pizza. Then the volume > of that pizza is equal to pi*z*z*a ! > ****************************************************************** ######################################################################## 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/
