ggsql: A grammar of graphics for SQL Introducing ggsql, a grammar of graphics for SQL that lets you describe visualizations directly inside SQL queries.

ggsql
opensource.posit.co/blog/2026-04...

SANOVA 公式HP - ピアノインストバンド ピアニスト堀江沙知による和製ジャズ・ピアノインストプロジェクト。

One of the my favorite music group is SANOVA.
horie2.wixsite.com/sanova

Current version of OpenFE supports SepTop protocol!
docs.openfree.energy/en/stable/tu...
Cool :)

🧪 Can LLMs judge chemical synthesis plans?

Excited to share new work from our industrial postdoc Varvara Voinarovska, in collaboration with Samuel Genheden and Mikhail Kabeshov at AstraZeneca's Molecular AI team!

📄 : doi.org/10.26434/che...

What’s DX…?

I can’t accept that it takes long time to open excel, pptx, word files in my office PC :(

ESI descriptors for scaffold hopping #memo #journal #LBDD #cheminformatics

Now there are some of Folding-AI such as AF3, Boltz and OpenFold3 is available to predict 3D structure of protein-ligand complex. So we can apply SBDD approach if we don't have experimental structures but there is still of…

Nanoscale Direct-to-Biology Optimization of Cdk2 Inhibitors Modern hit-to-lead optimization winnows down vast chemical spaces of virtual compounds into a selection of potent and selective compounds that can be further profiled with in vitro assays. Today, miniaturized chemical synthesis can be performed in high-throughput, shifting the bottleneck to compound purification. Direct-to-biology (D2B) approaches seek to overcome this hurdle by omitting the purification step and submitting reaction mixtures directly to bioassays. Here, we explore nanoscale hit-to-lead optimization through the multistep synthesis of a library of Cdk2/CycE inhibitors, utilizing ultrahigh-throughput experimentation (ultraHTE) in 1,536-well plates. Library performance is assessed by D2B in functional biochemical, bioaffinity, and X-ray crystallographic assays. A selection of potent lead Cdk2/CycE inhibitors identified by D2B was submitted to a phenotypic cell painting assay, which showed cell cycle arrest at G0, consistent with Cdk2 inhibition. This miniaturized workflow allows the upper tiers of a typical optimization screening cascade to be performed in a single experiment.

Nanoscale Direct-to-Biology Optimization of Cdk2 Inhibitors | Journal of Medicinal Chemistry pubs.acs.org/doi/pdf/10.1...

New Life for an Old Target: Melanin Concentrating Hormone (MCH) R1 Antagonists for Obesity For more than two decades, MCHR1 antagonists have been extensively investigated, but clinical progress has been hindered by toxicity and inadequate brain exposure. This Viewpoint highlights recent advances that have enabled the discovery of a novel MCHR1 antagonist with improved brain penetration and reduced toxicity, allowing it to advance into clinical trials.

New Life for an Old Target: Melanin Concentrating Hormone (MCH) R1 Antagonists for Obesity | Journal of Medicinal Chemistry pubs.acs.org/doi/10.1021/...

Use transformer model for Lead optimization #journal #memo

New fiscal year is stared from April. And I'm staying really busy days evenif my sum gradated his unior high school and volley ball team club 🙂 My role is changed now but still working around informatics area of drug discovery. Today I…

From my running course 😊

www.pnas.org/post/podcast...

15th RDKit UGM 2026 2026 RDKit User Group Meeting (in person and online)

Free registration for the 2026 #RDKit UGM (both in-person and online attendance) is now open:
www.eventbrite.com/e/1985889262...

Release 2026_03_1 (Q1 2026) Release · rdkit/rdkit Release_2026.03.1 (Changes relative to Release_2025.09.1) Acknowledgements (Note: I'm no longer attempting to manually curate names. If you would like to see your contribution acknowledged with you...

We did a new major #RDKit release yesterday. v2026.03.1 is out and the conda-forge builds are available.

As always, especially with major releases, be sure to read the "Backwards incompatible changes" section of the release notes!

github.com/rdkit/rdkit/...

Large-scale collaborative assessment of binding free energy calculations for drug discovery using OpenFE Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...

OpenFE is ready for production! chemrxiv.org/engage/chemr...

In collaboration with our industry partners, we ran benchmarking simulations of our hybrid-topology RBFE protocol on a large collection of both public and private protein-ligand binding datasets.

#compchem

Today, my eldest son successfully graduated from middle school :)

It’s not good to just launch it and then abandon it.

最初の立ち上げだけぶち上げてそのまま放り投げるの良くない。

Change heterocycle to another isoster with HCIE #memo #cheminformatics #RDKit Aromatic heterocycles are often used drug design as central core of molecule and they are often replaced another isosteric heterocycles for improvement of potency, ADMET or finding new IP space. Th…

Change heterocycle to another isoster with HCIE #memo #cheminformatics #RDKit iwatobipen.wordpress.com/2026/03/08/c...

Work led by industrial PhD student Sofia Larsson and in close collaboration with Susanne Winiwarter and @filipmiljkovic.bsky.social at AstraZeneca.

📄 Paper: chemrxiv.org/doi/full/10....
💻 Code: github.com/tsofiac/drug...
💽 Data: zenodo.org/records/1874...

The new #RDKit blog post is a guest post looking at doing Butina clustering on the GPU using nvMolKit.

greglandrum.github.io/rdkit-blog/p...

Rendering molecular image on Dataframe and Plot with marimo #Memo #RDKit #Cheminformatics As lots of readers know that RDKit has useful functions for coding with jupyter-lab. PandasTools and IPythonConsole is useful because by using these functions rdkit can render mol objects as SVG on…

iwatobipen.wordpress.com/2026/03/07/r...

It’s really surprising that Claude code works really hard :)

Shinagawa station is extremely crowded😱

Avogadro Stories (for 2.0 Release) As we finish up the 2.0 (final!) release, I’d like to feature some stories (and citations) about how Avogadro has shaped research and teaching. So if Avogadro has helped your research, please let me ...

Has @avogadro.cc helped your research? Teaching?

As we prepare Avogadro 2.0 for release this spring, I'm hoping to feature some stories (and citations).

#compchem #opensource #openscience ⚗️

Let me know:
discuss.avogadro.cc/t/avogadro-s...

It’s really difficult to understand for me that mixing quantum chemistry and quantum computing….

Small Molecule Statistics: Growth of Released Small Molecules per Year As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and adva...

www.rcsb.org/stats/growth...

Spending lots of time to modify same PDB and finally I could make image with ligting molecule.

still struggling blender :(

Happy to share our article on the PROTAC-Splitter, an ML framework for automated identification of PROTAC substructures, is now finally online in Journal of Cheminformatics! rdcu.be/e4Ulj 🤩

Work led by our amazing senior PhD student Stefano, together with collaborators at AstraZeneca. #chemsky