#cheminformatics — Public Fediverse posts

and hot on the heels, the CDK Scaffold extension had the 2.13 release too: https://doi.org/10.5281/zenodo.22000770

Based on CDK 2.13 and with some notes on how it handles stereochemistry and a fix. See https://github.com/cdk/cdk-scaffold/wiki/8.-Known-issues-with-stereochemistry-preservation#version-213 (and screenshot).

Full release notes here: https://github.com/cdk/cdk-scaffold/releases/tag/2.13

#chemistry #cheminformatics

CDK 2.13 was released: https://doi.org/10.5281/zenodo.21992083

- cdk-iordf now available separately
- more SMIRKS
- fragmenter for cicular substuctures
- reaction centers in MDL V2000
- CXSMILES coordinate bonds
- improved metal sandwich rendering

Full release notes: https://github.com/cdk/cdk/releases/tag/cdk-2.13

#chemistry #cheminformatics

RE: https://fosstodon.org/@zotero/117112205045153094

" ... and “h2o” will find “H₂O” and “H₂O”, and vice versa."

But will it do that too when I search for "XLYOFNOQVPJJNP-UHFFFAOYSA-N" ?

#chemistry #cheminformatics

Computational Biologist - Fully Remote
micro1

Computational Biologists (MSc or PhD) needed for fully remote contract work (up to $120/hour!). Ideally looking for experience in medicinal chemistry

See the full job description on jobRxiv: https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/

#bioinformatics #cheminformatics #computationalbiology #drugdiscovery #medicinalchemistry #S...
https://jobrxiv.org/job/micro1-27778-computational-biologist-fully-remote/?fsp_sid=14384

happy that I can now follow the InChI Trust posts here on #mastodon too now! @inchi-trust.bsky.social

#chemistry #cheminformatics #openscience

new blog: "Molecular Inorganics: SMILES, MDL molfile v3000, and InChIs" https://doi.org/10.59350/yhf27-fp921

"Both use the SMILES, but not all SMILES captures all the chemistry we need. And the InChI software needs an V3000 MDL Molfile. Thanks to John and other @cdk developers, there is good support for recent cheminformatics software, but I was not sure it had what I would need."

Replies to this post show up in the blog.

#chemistry #cheminformatics #inchi #openscience

I can do the same thing for polymers (here excluding the biopolymers): https://qlever.dev/wikidata/okph2M?exec=true

Again, with links to @Wikipedia and here, of course, using CXSMILES as preferred represenation

The question is, can this be used as input to create InChIs for these organometalics and polymers?

#chemistry #inchi #cheminformatics

I am at a technical InChI meeting, discussing about wonderful chemistry, such as organometalics. I am finding currently multiple organometalic compounds in @wikidata and @wikipedia: https://w.wiki/SgFB

What is your favorite organometalic compound in Wikipedia?

#chemistry #wikidata #wikipedia #inchi #cheminformatics

Extended-Connectivity Fingerprints in APL

Post: https://butwhyisthat.substack.com/p/ecfp
Code: https://github.com/manas02/ecfp

#cheminformatics

Our fingerprint analysis work has now been published 🎉 --> link.springer.com/article/10.1... Also check out our small helper library #chemap --> github.com/matchms/chemap (work together with @julianpollmann.bsky.social) #cheminformatics #openscience #Python

Count your bits: fingerprint b...

A newly developed evaluative framework that tests the reliability, transparency, and chemical reasoning of artificial intelligence (AI) models used in the development of new antibiotics.
#Cheminformatics #ComputationalBiology #Pharmacology #Microbiology #ArtificialIntelligence #sflorg
https://www.sflorg.com/2026/06/cobi06262601.html

ИИ в химии: история участия в хакатоне и рефлексия после

Всем привет! Меня зовут Константин Ушенин, я — ведущий научный сотрудник в AIRI, занимаюсь приложениями искусственного интеллекта в химии и фармакологии. В конце марта 2026 года мы с коллегами выиграли суточный хакатон от Сбера, ИТМО и СПБ ГБУ Молодёжного пространства «ПРОСТО» по созданию ИИ‑ассистента для планирования синтеза в лаборатории органической химии. Мероприятие прошло три месяца назад, однако мы завершили рефлексию результата только сейчас и решили сделать полный разбор. В этом посте вы узнаете про этапы нашей подготовки, выработку победной стратегии, решение проблем, возникавших по ходу соревнований, и наш подход к подготовке финальной презентации. В конце проведен анализ наших правильных и неправильных решений, а также дана оценка того, как реальное продуктовое решение должно отличаться от созданного на хакатоне. Но технологический ИИ‑стек на службе у химии — это не самое главное, о чём я хотел бы рассказать. Ключевую роль в нашей победе сыграла организация команды, распределение ролей и стрессоустойчивость всех её членов. Путь к первому месту оказался полным разных испытаний: начиная от неудобного стола и заканчивая хакерской атакой на наше решение за полчаса до защиты. В общем, получилось довольно остросюжетно, приятного чтения!

https://habr.com/ru/companies/airi/articles/1050580/

#hackaton #agentic_ai #chemistry #cheminformatics #llmагент #агентный_ии #хакатон

While playing around a bit more with @marimo_io's #molab, although I was able to make #RDKit work, it seems py3Dmol (https://pypi.org/project/py3Dmol/) does not work as it's supposed to (i.e. I can't get 3D molecules to display in the notebook). I likely may have missed other stuff that needs to be imported, so: has anyone else tried this combination and made it work?

(Otherwise, alternatives for making 3D molecules show up in molab are welcome!)

#chemistry #cheminformatics #python

If y'all would indulge me a late addition: the appropriate lines in the #RDKit code (https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Draw/__init__.py#L190-L224) can of course be modified to use the B&R blob I introduced in the essay.

What's hampering me from actually trying this out for myself is that due to RDKit not yet being supported by #Pyodide, a lot of the webservices that can run #Python from the browser (e.g. the online version of #jupyter) are also not able to load RDKit. (I have seen at least two proposals to use the JS version of RDKit instead, but I have not managed to make that work either.) Because I had written that essay, and am currently writing this toot from a smartphone (for a number of reasons, I don't have access to a computer I can use), indirectly using RDKit through Wolfram Cloud (basically the online version of Mathematica) is pretty much how I attempt to do cheminformatics experiments on a smartphone. :)

#chemistry #cheminformatics #visualization

I posted a short computational essay on Wolfram Community a little while ago (https://community.wolfram.com/groups/-/m/t/3727989) regarding what I call "molecular heatmaps" for visualizing atomic descriptors. This is based on previous work by #RDKit's Landrum and Riniker (cf. https://doi.org/10.1186/1758-2946-5-43).

Something I did not talk about in that essay is the virtue of reading journal articles that are outside of your usual purview (or, you might even say "comfort zone"). If I had completely restricted myself to the cheminformatics literature, I would not have found out about "blob functions" (cf. https://doi.org/10.1080/10867651.2001.10487549), which are often used in computer graphics. This isn't the first time I was able to profitably use knowledge from one subject to use in another one. It takes conscious effort, but I recommend having a wide reading appetite very warmly.

#chemistry #cheminformatics #visualization

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