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 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...

This week I updated an older #RDKit blog post to show how to use the RDKit in your own C++ projects on Windows. That post now covers Linux, the Mac, and Windows. greglandrum.github.io/rdkit-blog/p...

Save the date! Next year's European #RDKit UGM will take place from 16-18 September in Darmstadt, Germany. Pre-registration will open in early 2026.

The new #RDKit blog post shows off some reaction drawing tricks. greglandrum.github.io/rdkit-blog/p...

I forgot to post over the weekend... The new #RDKit blog post is a short one showing how to get decent 2D renderings for systems with intramolecular hydrogen bonds. greglandrum.github.io/rdkit-blog/p...

Yay! #RDKit

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...

It's great to see that the piles of money and enormous amounts of electricity and other resources used to train these models has produced such stunning and useful results. And I'm SUPER glad that google now always shows me this garbage.

It's always great to see a new release of ChEMBL appear!

This week I updated an older #RDKit blog post that demonstrates how to set things up so that you can easily use the RDKit in your own C++ code. greglandrum.github.io/rdkit-blog/p...

It's hard to believe that we're living in the future when things like this keep happening: me: "Hey Siri, put onions on the shopping list" Siri: "Ok, I put bananas on the shopping list"

Tonight I'm taking the train to Prague for the European edition of the 2025 #RDKit UGM. I'm really looking forward to meeting a bunch of the community there! We don't have space for any last-minute in-person registrations, but info on joining the live streams is here: github.com/rdkit/UGM_20...

This week's #RDKit blog post is a short one looking at the scaling of conformer generation time with the number of threads used. greglandrum.github.io/rdkit-blog/p...

Today's #RDKit blog post gets into the weeds of how inconsistent information in a common file format is handled by the RDKit. greglandrum.github.io/rdkit-blog/p...

I really like this description

well, I hope this little glitch is resolved soon.😕

What good is all the investment that Microsoft is making in AI if Windows keeps showing me that damn hummingbird image even though I click the "I don't like this" button EVERY SINGLE TIME it shows up?

I’m on vacation, so I asked an LLM to write this week’s #RDKit blog post. Here’s how it went greglandrum.github.io/rdkit-blog/p...

Today's #RDKit blog post shows a way to store partial charges in SD files. We really should stop using mol2 files. Thanks to @wpwalters.bsky.social for the inspiration for this one. greglandrum.github.io/rdkit-blog/p...

Today's #RDKit blog post is a heartfelt plea for clearer communication. greglandrum.github.io/rdkit-blog/p...

The new #RDKit blog post looks at two different approaches for picking a small number of diverse compounds from a large set. Sometimes you don't need to use the fancy way. greglandrum.github.io/rdkit-blog/p...

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...

The new #RDKit blog post, inspired by a question from @valencekjell.com, looks at the impact of molecular size on similarity thresholds. greglandrum.github.io/rdkit-blog/p...

This week's #RDKit blog post shows how to use some of the information added to molecules that come from the chemical reactions code. greglandrum.github.io/rdkit-blog/p...

The new #RDKit blog post is a guest post from @jemonat.fosstodon.org.ap.brid.gy with a tutorial on using Bemis-Murcko scaffolds. greglandrum.github.io/rdkit-blog/p...

This week I have updated and revised an old blog post showing how to perform extended Hueckel calculations with the #RDKit. This is a fun one for me because it involves work I did back in grad school. :-) greglandrum.github.io/rdkit-blog/p...

This #RDKit blog post builds on the earlier one about chemical words; this time I'm using Morgan fingerprint bits as the "words". greglandrum.github.io/rdkit-blog/p...

The new #RDKit blog posts demonstrates how to work with your own fingerprints in the PostgreSQL cartridge. greglandrum.github.io/rdkit-blog/p...

This week's #RDKit blog post revisits and updates a really old post looking at the most common chemical "words". greglandrum.github.io/rdkit-blog/p...

TFW you realize that you built a *bunch* of models using sklearn's RandomForestRegressor using default params, which, of course, means that you didn't actually build random forests. 🤦 Ah well, they don't take that long to build and the real random forests build even faster.

This week's #RDKit blog post is an updated and revised version of a very old one looking at the options for constructing molecules more efficiently. greglandrum.github.io/rdkit-blog/p...

The new #RDKit blog post is a tutorial on how to specify atomic property changes when using chemical reactions. greglandrum.github.io/rdkit-blog/p...

Confused about enhanced enhanced stereochemistry in cheminformatics? The new #RDKit blog post shows a prototype of a tool to help visualize/explain what an enhanced stereo specification actually means. greglandrum.github.io/rdkit-blog/p...

The new #RDKit blog post builds on the recent one about similarity hit set overlaps by taking similarity noise levels into account. greglandrum.github.io/rdkit-blog/p...

This week's short #RDKit blog post introduces some new functionality for interrupting long-running calculations. greglandrum.github.io/rdkit-blog/p...

The new #RDKit blog post is an update of an older tutorial on displaying fingerprint bits. greglandrum.github.io/rdkit-blog/p...

The new #RDKit blog post is an exploration of how much overlap there is in the hit lists of similarity searches done using different fingerprints. This is the data supporting the argument "it's useful to combine results from different FPs" greglandrum.github.io/rdkit-blog/p...

The new #RDKit blog post is an updated tutorial on constructing simple SAR tables in Jupyter notebooks: greglandrum.github.io/rdkit-blog/p...

Pre-registration for the 2025 #RDKit UGM, to be held from 10-12 September in Prague, is now open! The link is below. Note that registration is a two-step process this year; there's more information in the form itself. forms.gle/pu7ELeUwARFQ...

In a new Practical Cheminformatics post titled "Even More Thoughts on ML Method Comparisons," I share several plots that I find valuable for comparing machine learning methods. practicalcheminformatics.blogspot.com/2025/03/even...

The requests from notion to be allowed access to location info are really increasing my motivation to look at obsidian more seriously.

I love the thought of putting together some well-curated and standardized datasets for use in benchmarking/validating methods, but I am never going to either use them myself or encourage others to use them if I have to log in to download the data. I'm looking at you @polarishub.io

This week's #RDKit blog post shows how to use the built-in drawing code to create a more complex figure. greglandrum.github.io/rdkit-blog/p...

😢

Today's #RDKit blog post is a tutorial on using the AdjustQueryProperties function to have more control over substructure queries greglandrum.github.io/rdkit-blog/p...

The new #RDKit blog post is a tutorial on highlighting atoms in molecular drawings. greglandrum.github.io/rdkit-blog/p...

Why oh why is this nonsense in zoom now? I just want a good tool for doing online meetings.

I have my nice worksheet with images of compound structures and a bunch of data open in Excel and then I stop paying attention for one second and click "sort". Now there are images randomly distributed in that column and deleting the column doesn't delete the screwed up images. Rookie mistake

Our new paper in JACS presents the application of a new neural network potential, based on our anisotropic message passing approach, to do QM/MM MD simulations. We achieve chemical accuracy on a few quite different types of chemistry. doi.org/10.1021/jacs... #chemsky #compchem #opensource