I wrote about it in a blog post here: tlint101.github.io/practice-in-... (It is basically the tutorial section, but it counts!)

My first post and I would like to plug my project - pharmacophore-toolkit. I thought others in the #cheminformatics, #molecularmodeling, #drugdiscovery, or the #chemsky #compchem community would find it helpful. github.com/tlint101/pha...

AI is an extremely useful tool, but it consumes vast amounts of energy and impacts the environment. Can we balance technological progress with environmental conservation?

Neurons can communicate via hidden network of nanotubes, study finds | Science | AAAS www.science.org/content/arti...

Now we can use compiled version of mmseq from original repo. github.com/soedinglab/m... I would like to test the perfomance on HPC environment.

Leveraging Structural and Computational Biology for Molecular Glue Discovery | Journal of Medicinal Chemistry pubs.acs.org/doi/10.1021/...

This week's #RDKit blog post shows how to create simple protein--ligand interaction diagrams. I think there's potential to take this a bit further... greglandrum.github.io/rdkit-blog/p...

I'm making curry and rice for dinner! Also I'm making material for cheminformatics tutorial of next month.

GPU based fast Shape alignment of molecules #RDKit #Roshambo2 #Cheminformatics Most of readers know that power of GPU change the way of cheminformatics. I introduced nvMolkit which is developed by NVIDIA for cheminformatics tasks. Now we can handle huge amount of data in short time 🙂 nvMolKit can…

Many people love the word ‘DX’ but most of them don’t like change something. It’s difficult to understand for me 🤫

Rust 1.90.0 is out! blog.rust-lang.org/2025/09/18/R... Major features: * lld as the default linker on x86_64-unknown-linux-gnu * cargo workspace publishing support built into cargo * more const context APIs, and stabilization of new useful APIs

Published yesterday In Nature: DeepSeek-R1 incentivizes reasoning in LLMs through reinforcement learning www.nature.com/articles/s41... 🧪

I dislike clinging to inefficient practices and resisting change.

RDKit meets GPU #RDKit #nvmolkit #nvidia #cheminformatics Unfortunately I could not participate RDKit UGM 2025 in this year.... I would like to join the meeting at next year By the way, recently we can use GPUs for acceralate chem/bio informatics calculations such as Deep Learning application or…

It is really cool!!!!11 nvMolKit is a CUDA-backed python library for accelerating common RDKit molecular operations. t.co/GQYcAnIVTd

Building new docker container via iPhone

I love music of fox capture plan music.apple.com/jp/album/but...

AI driven drug discovery works well if lots of information for the target is available such as Kinase. I would like to know example for novel target.

github.com/rdkit/UGM_2025 Virtual attendance As in years past, we will live stream the UGM over zoom. Unlike in previous years, virtual attendance does not require registration.

This chart is a one of AI pharma stock price over 5 years. AI based drug discovery is growing up rapidly but it don't contribute human health at the moment IMHO... I hope AI originated drug contribute human health near the feature.

Deep Learning process goes well even if I can use only GPU which has samll vRAM :)

Finally I could run test code for GNN.

How to make training data from tacit knowledge in medicinal chemistry is one of the big challenges.

Notes and a pelican for DeepSeek 3.1 simonwillison.net/2025/Aug/22/...

Contribute open science #memo #dirary I am enjoying a weekend with free time for the first time in a while 🙂And I checked my blog site and found that I stared the site from 2012/08/10. So it means that I've kept writing blog for almost 13 years. When I stareted the blog post I was a wet medicinal…

It is not equal that promoteing DX and purchace new IT tools ...

When I use large data set I need incread heap space. www.knime.com/faq#q4_2

　Useful workflow of medicinal chemistry knowledge #Knime #Cheminformatics #MMP Bioisosteric replacement is one of the important strategy for drug design. For example improve biological activity without any affect to ADME properties or improve ADME properties without reducing biological activities.…

I'm really happy because my sun qualified for the national tournament of vollyball! He will go Nagasaki in this week. It will be busy but exciting summer vacation for him :) (also for me..)

MMseqs2 v18 is out - SIMD FW/BW alignment (preprint soon!) - Sub. Mat. λ calculator by Eric Dawson - Faster ARM SW by Alexander Nesterovskiy - MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API) 💾 github.com/soedinglab/M... & 🐍

Transferring Knowledge from MM to QM: A Graph Neural Network-Based Implicit Solvent Model for Small Organic Molecules | Journal of Chemical Theory and Computation pubs.acs.org/doi/10.1021/...

The more a project goes wrong, the more people try to avoid responsibility. But it's difficult to explaine the reason with only one reason.

It seems interesting. Combination of fragment and LLM for drug design. arxiv.org/pdf/2507.13580 Repo is opened but code isn’t available now

New code for evaluating ligand strain calculation #RDKit #StrainRelief #Cheminfo Japanese summer is very hot and humid most days. It's not so good for running.It's important to stay hydrated. I'm keeping my lunch time 5km Running when I work from home. I could have time to read scientific articles…

The new #RDKit blog post is another exploration of the impact of molecule size on similarity; this time looking at single-atom changes. greglandrum.github.io/rdkit-blog/p...

Platt et al. Development and Evaluation of High Affinity Peptide-Drug Conjugate Ligands for the TRIM24 PHD and Bromodomain chemrxiv.org/engage/api-g...

Zhang et al. A Large Language Model for Chemistry and Retrosynthesis Predictions arxiv.org/pdf/2507.01444