It’s snowing here for the first time in about over 10 years.

Split PROTAC molecule to 3 compornents with protac_splitter #RDKit #cheminfomratics #memo #python Proteolysis-targeting chimeras (PROTACs) are one of the interesting modalities in these days because the modality can engage protein of interest (POI) and E3 ubiquitin ligase and then causes…

A Comprehensive Review of Emerging Approaches in Machine Learning for De Novo PROTAC Design arxiv.org/abs/2406.16681

Protap: A Benchmark for Protein Modeling on Realistic Downstream Applications arxiv.org/abs/2506.02052

Blogpost that looks at how LLMs have improved at 'reasoning' over time. This is a key capability that enables many scientific workflows. baoilleach.blogspot.com/2026/01/impr...

A reminder that proteins are highly dynamic molecules. 🟧 We have made much progress in measuring & predicting static protein structures, but the dynamics that animate life remain challenging to measure & model.

Manager "We would lile to develop expert MedChem AI which can design molecules efficientry! Cheminformatician(like me) should develop it!" MedChem "We don't beleave AI! It proposes strange molecules" Me "Hmmmm... it's difficult to solve the issue.."

New clustering algorithm for cheminformatics #bblean #cheminformatics #RDKit Clustering is one of the common but really important task of cheminformatics. There are lots of clustering algorithms are know as readers know, but now we should struggle with huge amount of compound dataset such as…

New version is released! github.com/dptech-corp/...

More data is required to obtain more accurate AI for drug discovery but we need to reduce cost of experiments. BTW, if you would like to use accurate simulation such as FEP, you need more budgets to get suitable computational resources.

Can AI become a powerful new tool for chemistry? A PNAS Special Feature explores how machine learning is transforming drug design, materials discovery, and molecular prediction, while also exploring the challenges that limit broader adoption. Read the blog post: https://ow.ly/YZvz50XR9JC

Useful utils for analysing chemical reaction #cheminformatics #rdkit #rxnutils Recently lots of users know that generative model of molecule is really useful for drug design. But one of the big challenge is how to make designed molecules. So predicting sythetic route AI is hot topics in these area…

I don't think I can do good work with someone who, despite being talented, lacks empathy.

Enjoying glamping with my family 👍

10km jog ✅

Look Back at 2025 #diary I’m writing this post at 20:30 ~ JST. I would like to look back at 2025 in my blog post 😉 RunningIn this year my running total distance was 1078km. It was shorter than last year. It is as same as 2024. It was lack of long distance running at weekend. I would like to keep…

Considering predictive models for using cheminfomratics tasks #cheminfomratics #memo #journal In this, year my role is changed from resarcher to manager. It's really big change for　better or worse... Fortunately I'm still working in cheminformatics field 🙂 And in this year I could have an…

Analysis of phase II and phase III clinical trial terminations from 2013 to 2023 www.nature.com/articles/d41...

Realy cooooooooooooooooool

My eldest son was able to finish the last tournament of the year with a victory. :)

Today's #RDKit blog post is a tutorial/explanation about which atoms are considered as candidates for tetrahedral chirality. greglandrum.github.io/rdkit-blog/p...

5km run at morning

This week's #RDKit blog post, like last week's, looks at creating your own synthon spaces. Last week was BRICS, this week we use some combichem reactions: greglandrum.github.io/rdkit-blog/p...

Use joblib with free-threaded python #memo #diary Python 3.14 was released on 7 October 2025. The new version of python support for free-threaded (No GIL). I asked it about AI and reasonable description shown below. To understand the merit of "No-GIL" Python (officially known as free-threaded…

Suitable investments are required not only AI technology but also data collection technology to promote AI driven drug discovery (IMHO). Because data is new oil.

There is quite a bit of AI skepticism on chemsky, and reasonably so - but it is very interesting to see /another/ chemistry AI startup (Excelsior Sciences) get bigtime funding ($95M): cen.acs.org/physical-che... by @cenmag.bsky.social's Aayushi Pratap #chemchat

The Latest in Automated Analog Generation | Science | AAAS www.science.org/content/blog...

I started my blog post 16 years ago! It's really amazing that I can keep it :)

ourworldindata.org/brief-histor... Worth to read!

Similarity screening with RDKit #RDKit #SimilarityScreener #memo #cheminformatics Similarity based screening is one of the common way to explore SAR rapidly. For example if you got hit compound but lack of human resources for making analogue compounds, catalogue SAR is useful way to expand SAR. Of…

12km jog ✅

This week's #RDKit blog post continues my look at the LOBSTER data set. This one got a bit derailed because I found a bug while working on it. greglandrum.github.io/rdkit-blog/p...

I tried to install Openforld3 to my personal computer with pixi. It succeeded. I canceld the process because size of parameters were too big. So I will try again on HPC env tomorrow.

This week's #RDKit blog post looks at LOBSTER, a nice molecular superposition data set that came out last year. Now that everything's loaded into a database using lwreg, I can start playing with the data in future posts. greglandrum.github.io/rdkit-blog/p...

I got shuffled around different departments with no solution. It is really tough for me...

Install roshambo2 to pixi env #memo #cheminformatics #RDKit Recently I'm using pixi for environment managment. Because it works very fast and can handle not only conda but also pypi in local .pixi env. Today, I tried to install roshambo2 to pixi env. The original article is published from JCIM and…

Era of open science medium.com/@dapscience/...

I know some people have had problems accessing the discord servers we use for the UGMs, so I'm trying an experiment with setting up a Zulip server for the #RDKit. If this works well, we can leave it up as an informal chat/discussion point for the community. rdkit.zulipchat.com/join/ay4ccup...

Science is standing on the shoulders of giants. I respect pior arts of all scientific researches.

Photos from today’s running

I could have a fruitful discussion about AI driven drug discovery last week. And found that main issue for promoting AI driven drug discovery is not changed over 20 years :P It is a nightmare...

Run MD simulation with Openff&Openmm on pixi’s env #cheminformatics #RDKit #pixi #memo My background was organic chemistry but now I'm working as cheminformatitian. So I have lots of experiences of cheminformatics and medicinal chemistry but not many experiences of molecular simulation. But I'm…

Build environment from github repository with pixi #cheminformatics #memo #pixi I could have really fruitful discussions last week at CBI2025 annual meeting. Really appreciate all participants and presenters. I realized that I love open science and I would like to contribute it 🙂 I wrote new…