Egon Willighagen#SWAT4HCLS is over.
Today, I am at the #KNCV CTC meeting, where we are launching the #Cheminformatics and #DrugDiscovery working group, as part of the CTC Section
JH shows recent work where they use LLMs together with chemical similarity knowledge to do ChEBI ontology classification, the chebifier: https://chebifier.hastingslab.org/ and https://doi.org/10.1039/D3DD00238A
ICCSTwo papers for the ICCS Collection in the Journal of Cheminformatics have been tagged as accepted now. With another 4 under review, and at least one more paper to be submitted. The deadline was extended one last time.
But we are looking forward to a nice collection of work presented at the ICCS 2025!
Blue ObeliskOPSIN 2.9.0 has been released: https://chembl.blogspot.com/2026/03/opsin-v290-released.html
OPSIN is an IUPAC name parser that returns SMILES
"The release notes describe a mixture of minor bug fixes and improvements:"
Andrew DalkeHere's an #RDKit #cheminformatics quiz for you all. What do you think this code will output?
from rdkit import Chem
mol = Chem.MolFromSmiles("C" + "C(C)(C)" * 50 + "C")
pat = Chem.MolFromSmarts("[$([CD4H0X4](-*)(-*)(-*)-*)]")
print(len(mol.GetSubstructMatches(pat)))
No cheating by actually running the code! :) Feel free to explain your reasoning in the comments.
0
38
42
50
Poll ended at .
Spent most of the week writing an EState count #cheminformatics fingerprint for #chemfp .
It should have been a few hours to build on RDKit's EState code. Perhaps a bit longer to implement a faster version using the same SMARTS patterns.
I then realized the RDKit implementation and patterns had problems, eg, not matching both atoms in "CC", and unexpected handling of explicit hydrogens, like in deuterated [2H]. See https://git.sr.ht/~dalke/rdkit/log
The hard part was finding good test cases.
SureChEMBL has the banner "By using the site you are agreeing to our Privacy Policy". It links to https://chembl.gitbook.io/surechembl/privacy-notices then https://chembl.gitbook.io/surechembl/privacy-notices/surechembl-website links then https://1396459327-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fty0JOfWwPnEbs5wW271w%2Fuploads%2F8dCXtuh9PSd4NKw4f7Cd%2FPrivacy%20Notice%20SureChEMBL%20website.pdf?alt=media&token=bc640502-e42a-4776-92e7-24ea3e871380
They use Google Analytics to track my visit.
I sent email to the #EMBL data controller via [email protected] to highlight issues with Google and the US, and asked they stop using Google Analytics, or clarify why they couldn't use one of https://european-alternatives.eu/alternatives-to .
You should email them too. #cheminformatics
pyBacting 0.2.16 (with CDK 2.12) is now available at https://pypi.org/project/pybacting/
CDK 2.12 blogpost https://chem-bla-ics.linkedchemistry.info/2026/03/08/cdk-2.12.html https://doi.org/10.59350/gw9at-srp84
Replies will show up in the blog
"LOTUS Wikidata Explorer" https://adafede.github.io/marimo/apps/lotus_wikidata_explorer.html (by @adafede)
