Euclid 2.14 is released: https://doi.org/10.5281/zenodo.17996224 https://github.com/BlueObelisk/euclid/releases/tag/euclid-2.14

Minor update with upgraded dependencies to Log4j 2.25.3 and Commons IO 2.21 and Lang3 3.20.

Euclid is a library of numeric, geometric and XML routines.

#java #cheminformatics

I just submitted a #cheminformatics preprint to ChemRxiv, based on the #RDKit count fingerprints, #chemfp, and some one-off R&D code I wrote over the last few months.

"Superimposed Coding of Count Fingerprints to Binary Fingerprints"

In short, my superimposed coding method gives k-recall@k nearest neighbor scores ~0.9 relative to using full count fingerprints and the multiset Tanimoto (aka MinMax, aka Ruzicka similarity). Recall can be over 0.95 w/ 8192 bits!

https://chemfp.com/SuperimposedCounts.pdf

#OpenBabel is dead, long live #RDKit!

https://github.com/RMeli/spyrmsd/issues/149

On a more serius note, it would be cool to have a cheminformatics library that actually works. Don't get me wrong, RDKit is very cool - but you can feel all the underlying problems it has when using it.

#Cheminformatics

💐👏 Congratulations to Sabrina Jaeger-Honz from our Project D04! She won the Airbus Research Award "Claude Dornier" for her #dissertation "Combining Bio- and Cheminformatics for Small Data Sets: Microcystins as a Use Case".

💡 Using computational methods, Sabrina's thesis presents multiple interconnected approaches in order to overcome difficulties associated with studying small datasets in bio- and #cheminformatics.

➡️ https://www.sfbtrr161.de/news/Airbus-Forschungspreis-Claude-Dornier-for-Sabrina-Jaeger-Honz/

#sfbtrr161 #visualcomputing

🤖 What happens when we let a Transformer model, not a docking engine, judge protein–ligand affinity?

🔗 DrugForm-DTA: Towards real-world drug-target binding affinity model. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.09.023

📚 CSBJ: https://www.csbj.org/

#DrugDevelopment #DrugDiscovery #Cheminformatics #StructuralBiology #ChemicalBiology #DrugTargetAffinity #QSAR

🤖 Can AI help us predict and prevent off-target effects in PROTAC drug design?

🔗 Predicting PROTAC off-target effects via warhead involvement levels in drug–target interactions using graph attention neural networks. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.028

📚 CSBJ: https://www.csbj.org/

#DrugDevelopment #StructuralBiology #ChemicalBiology #PROTAC #DrugDiscovery #Cheminformatics #Bioinformatics #PrecisionMedicine #TargetedProteinDegradation

new blog: "WikiPathways curation reports on profile pages" https://doi.org/10.59350/s7vw2-r7y02 https://chem-bla-ics.linkedchemistry.info/2025/11/30/wikipathways-curation-reports-on-profile-pages.html

Replies to this post show up as comments in the blog post.

#bioinformatics #cheminformatics #curation

The submission deadline for the ICCS Collection in the Journal of Cheminformatics will be extended to March 1. We currently have four papers under review and expect at 2 more submissions.

https://link.springer.com/collections/jcfcedbfda

#cheminformatics #iccs2025

Yesterday, we were very happy to host the November meeting of the InChI developer team at the Beilstein-Institut. Many thanks to the Aachen side of the InChI team for coming to Frankfurt!

Find out more about our #BeilsteinCheminfoLabs projects where we are supporting InChI and other open source projects ➡️ https://www.beilstein-institut.de/en/projects/cheminfo-labs/inchi/?M=y

#inchi #cheminformatics #chemistrystandards #iupacinchi