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

Euclid

Minor update with upgraded dependencies to Log4j 2.25.3 and Commons IO 2.21 and Lang3 3.20. Full Changelog: https://github.com/BlueObelisk/euclid/compare/euclid-2.13...euclid-2.14

Zenodo

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

Remove Open Babel support? · Issue #149 · RMeli/spyrmsd

Open Babel seems to have become abandonware. The last commit on master is from December 2024. The last release on GitHub is from 2020, and the same goes for the last release in PyPI. Open Babel is ...

GitHub
If you've money left in your #cheminformatics, #chemfp makes a nice Christmas present. :)

💐👏 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

Research from the 13th International Conference on Chemical Structures

The 13th International Conference on Chemical Structures (ICCS 2025) will take place on June 1-5, 2025, in Noordwijkerhout, The Netherlands, where it has been ...

SpringerLink

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