the third paper in the #iccs2025 collection is out: https://doi.org/10.1186/s13321-026-01203-8

"GRIPHIN: grids of pharmacophore interaction fields for affinity prediction"

"We investigate whether a purely pharmacophoric representation of the protein pocket is sufficient to train a deep learning model for affinity prediction. For this purpose, we devise a hybrid model architecture from simple building blocks for affinity prediction."

#cheminformatics #drugdiscovery

RE: https://fediscience.org/@ElenLeFoll/116605736856479038

chemists too, plz! #chemistry #cheminformatics

🚀 Chemists spend too much time on tools – instead of letting them do the work for them.

This video shows you how to draw molecules, convert formats and analyse substructures – faster and smarter.

👉 youtu.be/HfMY4BA54X8

#Chemistry #Cheminformatics #Productivity

new blog post: "One Million IUPAC names #5: a new approach and 400k names" https://doi.org/10.59350/gqtbx-jta57 #openaccess #iupac #cheminformatics #blueObelisk

"Europe PMC, however, also provides the JATS XML files as download on their FTP site. Already that august 2025 I had a prototype and knew it would change the game. These gzipped XML files are about 150 to 250 MB. Unzipped, about 1 GB each."

Replies to this post show up in the blog.

Did you know that the Beilstein-Institut has always been a digital innovator in chemistry - from the Beilstein Database in the ‘80s to the digital infrastructure and standards in chemistry projects supported in the current Beilstein ChemInfo Labs 🧪💻?

➡️ https://www.beilstein-institut.de/en/projects/cheminfo-labs/?M=y

Join us in making chemical data accessible, findable, and reusable for everyone.

#BeilsteinChemInfoLabs #OpenScience #Cheminformatics #FAIRData #STRENDA #MIRAGE #Beilstein75

what is the flagship *diamond* #openaccess journal in the fields of #cheminformatics and/or #bioinformatics ?

1. flagship := solid peer review, good editorial standards, innovative, etc (and I care about citations to our work, not JIFs)
2. diamond := zero APC and not prepaid APC

#openscience

Williams and Richard, https://doi.org/10.1186/s13321-025-00983-9

Pillar 1: Government funding and public support for structure-indexed, searchable, downloadable chemical databases

Pillar 2: clear data licensing, provenance, and the need for FAIRness

Pillar 3: Coordinated community approaches regarding structure formats, ontologies, and quality curation procedures to ensure accurate association of chemical substances with associated identifiers, including structures, chemical names [..]

#cheminformatics

a macro to generate other macros was the best idea ever: now confirmed

(with the last version of emacs-indigo for pretty-much-memory-safe molecule manipulation inside emacs!)

https://github.com/gicrisf/emacs-indigo

#emacs #lisp #chemistry #cheminformatics #metaprogramming #programming #code #coding #fp

🧩 Could RNA and proteins share the same “shape language” for binding drugs?

🔗 Eigenvalue Ratios Reveal Shared Binding Pocket Shapes in RNA and Protein Structures. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0022

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#DrugDiscovery #StructuralBiology #ComputationalBiology #RNAResearch #ProteinScience #Bioinformatics #MolecularModeling #Genomics #Proteomics #Cheminformatics #LigandBinding