Lightnews — Scholar-powered news

Greg Landrum @greglandrum.bsky.social · 1d

Coffee and tea are substitutes for each other?!?!?
<sigh> economists...

Greg Landrum @greglandrum.bsky.social · 5d

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...

Rendering intramolecular H bonds in 2D – RDKit blog

A simple approach to get nonbonded atoms close to each other.

greglandrum.github.io

1 1 10

Greg Landrum @greglandrum.bsky.social · 10d

Now that we include new features in the minor releases, the big ones aren't quite so dramatic, but it's still a great feeling to get one out the door.

6

Greg Landrum @greglandrum.bsky.social · 10d

Yay! #RDKit

A screenshot showing that my "rdkit_new" conda environment is running the 2025.09.1 RDKit release

1 1 10

Greg Landrum @greglandrum.bsky.social · 14d

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...

Drawing simple protein–ligand interaction diagrams with the RDKit – RDKit blog

Quick, but useful

greglandrum.github.io

4 15

Greg Landrum @greglandrum.bsky.social · 15d

It actually makes be a bit sad. I still vividly remember when google first appeared and how transformational it was. What do you mean that I no longer have to put "-sex" in every query string on Altavista in order to not drown in porn results for my science query?!?!?

3

Greg Landrum @greglandrum.bsky.social · 15d

That requires me to either know that I want a pace chart or to do math.
The first couple of hits are all useful for answering the question.

1

Greg Landrum @greglandrum.bsky.social · 15d

🫠

Greg Landrum @greglandrum.bsky.social · 15d

ecosia isn't terrible

1

Greg Landrum @greglandrum.bsky.social · 15d

My normal solution is to just not use google for web search any more.
If they insist upon abusing me (and destroying the open web), why should I support them?
I just hadn't updated my search prefs on this computer, so I was surprised by the slop

1 2

Greg Landrum @greglandrum.bsky.social · 15d

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.

A screenshot showing the AI Overview result for the google query. "What is the required pace for a 2:10 marathon"
The AI-generated answer is egregiously wrong.

4 9 20

Greg Landrum @greglandrum.bsky.social · 17d

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

Chemical Biology Services @chembl.bsky.social · 17d

ChEMBL 36 is out!

chembl.blogspot.com/2025/09/chem...

ChEMBL 36 is out!

📊 Database Scale 🆕 New Data Sources Src_ID 72 – Chemical Probe data from Scientific Literature NLP and manual extraction from probe-r...

chembl.blogspot.com

1 5

Greg Landrum @greglandrum.bsky.social · 21d

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...

Using the RDKit in a C++ program – RDKit blog

It’s actually pretty easy

greglandrum.github.io

8

Greg Landrum @greglandrum.bsky.social · 22d

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"

2

Greg Landrum @greglandrum.bsky.social · Sep 8

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...

GitHub - rdkit/UGM_2025: 2025 RDKit UGM

2025 RDKit UGM. Contribute to rdkit/UGM_2025 development by creating an account on GitHub.

github.com

4 13

Greg Landrum @greglandrum.bsky.social · Aug 30

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...

Scaling conformer generation – RDKit blog

How many cores should I use for conformer generation?

greglandrum.github.io

7

Greg Landrum @greglandrum.bsky.social · Aug 22

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...

How the 2D/3D flag in Mol blocks is used – RDKit blog

Specifications meet the real world

greglandrum.github.io

2

Greg Landrum @greglandrum.bsky.social · Aug 21

I happily used Marvin as my primary sketcher for years. Having Linux support was key for me. Only stopped when they recently decided to no longer sell single licenses.

3

Greg Landrum @greglandrum.bsky.social · Aug 18

I think that even when you take innovation and experience into account, you're still going to have a giant bulge in the middle for exploration and actually doing the work.

1 1

Greg Landrum @greglandrum.bsky.social · Aug 18

I really like this description

Itai Yanai @itaiyanai.bsky.social · Aug 18

The difference between doing a project and presenting it. An observation can lead to many avenues of explorations before focus turns to a specific discovery. Presenting it, in a talk / paper, follows inversely, with broad perspectives coming before & after the specific discovery.

1 1 2

Greg Landrum @greglandrum.bsky.social · Aug 12

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

screenshot showing now open pull requests on the main RDKit repository

1 1

Greg Landrum @greglandrum.bsky.social · Aug 12

This is the one on the lock screen, and I like the *other* pictures... it's just the birds! :-)

1

Greg Landrum @greglandrum.bsky.social · Aug 12

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?

3 1

Greg Landrum @greglandrum.bsky.social · Aug 10

(c) the version of Temple of Love on it is different enough from the original to almost be a different song. :-)

1

Greg Landrum @greglandrum.bsky.social · Jul 31

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...

An LLM experiment – RDKit blog

What happens if you ask an LLM to generate an RDKit blog post?

greglandrum.github.io

7