Greg Landrum
@greglandrum.bsky.social
Cheminformatician, developer, climber, runner, hiker, cook
ORCID: 0000-0001-6279-4481
ORCID: 0000-0001-6279-4481
I really enjoy my birthday, but this time I have had a particular Sammy Hagar song popping into my head for the last few days, and I'm very much ready to be done with it
December 29, 2025 at 12:36 PM
I really enjoy my birthday, but this time I have had a particular Sammy Hagar song popping into my head for the last few days, and I'm very much ready to be done with it
The last #RDKit blog post of the year is a brief look back at 2025.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Wrapping up 2025 – RDKit blog
Completing the streak
greglandrum.github.io
December 28, 2025 at 6:28 AM
The last #RDKit blog post of the year is a brief look back at 2025.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
I’m hard at work on this week’s blog post.
December 27, 2025 at 5:49 PM
I’m hard at work on this week’s blog post.
I keep taking pictures like this in this gorge. Goodness do I love 🧗here.
December 22, 2025 at 6:00 PM
I keep taking pictures like this in this gorge. Goodness do I love 🧗here.
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...
greglandrum.github.io/rdkit-blog/p...
About tetrahedral chirality in the RDKit – RDKit blog
Answering a frequently asked question
greglandrum.github.io
December 21, 2025 at 8:48 AM
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...
greglandrum.github.io/rdkit-blog/p...
Wow, the LinkedIn year in review was even dumber than I thought it was going to be.
Maybe not everyone needs to do this.
Maybe not everyone needs to do this.
December 17, 2025 at 11:20 AM
Wow, the LinkedIn year in review was even dumber than I thought it was going to be.
Maybe not everyone needs to do this.
Maybe not everyone needs to do this.
@polarishub.io I'm starting a new project and wanted to use the Fang (a.k.a. Biogen) data set. Since I'm starting from scratch, this tim I figured I'd try grabbing it from polaris instead of doing my own curation. 1/n
December 16, 2025 at 7:03 AM
@polarishub.io I'm starting a new project and wanted to use the Fang (a.k.a. Biogen) data set. Since I'm starting from scratch, this tim I figured I'd try grabbing it from polaris instead of doing my own curation. 1/n
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...
greglandrum.github.io/rdkit-blog/p...
Building synthon spaces with combinatorial reactions – RDKit blog
A frequently requested tutorial part 2
greglandrum.github.io
December 14, 2025 at 5:36 AM
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...
greglandrum.github.io/rdkit-blog/p...
This week's #RDKit blog post is an attempt to figure out thresholds for meaningful "similarity" with 3D methods. I think there may be a bit of tweaking to do here, but it's a start.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Thresholds for “random” with 3D similarity methods – RDKit blog
What is noise in 3D?
greglandrum.github.io
November 30, 2025 at 1:27 PM
This week's #RDKit blog post is an attempt to figure out thresholds for meaningful "similarity" with 3D methods. I think there may be a bit of tweaking to do here, but it's a start.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
This week's #RDKit blog post is the third in a series using the LOBSTER data set.
This time I use the data to compare 3D alignment methods.
greglandrum.github.io/rdkit-blog/p...
This time I use the data to compare 3D alignment methods.
greglandrum.github.io/rdkit-blog/p...
Working with the LOBSTER Data set III – RDKit blog
Comparing 3D alignment methods.
greglandrum.github.io
November 23, 2025 at 6:09 AM
This week's #RDKit blog post is the third in a series using the LOBSTER data set.
This time I use the data to compare 3D alignment methods.
greglandrum.github.io/rdkit-blog/p...
This time I use the data to compare 3D alignment methods.
greglandrum.github.io/rdkit-blog/p...
Am I the only one getting a cloudflare error when they try to access ACS publications?
November 18, 2025 at 2:17 PM
Am I the only one getting a cloudflare error when they try to access ACS publications?
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...
greglandrum.github.io/rdkit-blog/p...
Working with the LOBSTER Data set II – RDKit blog
Conformer generation and comparing 3D fingerprints
greglandrum.github.io
November 17, 2025 at 5:47 AM
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...
greglandrum.github.io/rdkit-blog/p...
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...
greglandrum.github.io/rdkit-blog/p...
Working with the LOBSTER Data set I – RDKit blog
Registering and working with a 3D data set using lwreg
greglandrum.github.io
November 8, 2025 at 4:38 PM
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...
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...
If this works well, we can leave it up as an informal chat/discussion point for the community.
rdkit.zulipchat.com/join/ay4ccup...
RDKit
Zulip organization for the RDKit community
rdkit.zulipchat.com
November 6, 2025 at 5:54 AM
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...
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...
greglandrum.github.io/rdkit-blog/p...
Using the RDKit in a C++ program – RDKit blog
It’s actually pretty easy
greglandrum.github.io
October 23, 2025 at 1:25 PM
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...
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.
Pre-registration will open in early 2026.
October 21, 2025 at 3:25 PM
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.
Pre-registration will open in early 2026.
The new #RDKit blog post shows off some reaction drawing tricks.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Displaying atom maps and highlighting with reactions – RDKit blog
How to display info about a reaction transformation on a set of specific reactants and products.
greglandrum.github.io
October 17, 2025 at 6:41 PM
The new #RDKit blog post shows off some reaction drawing tricks.
greglandrum.github.io/rdkit-blog/p...
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...
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
October 6, 2025 at 3:53 AM
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...
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...
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 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
September 26, 2025 at 3:58 PM
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 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.
September 25, 2025 at 3:40 PM
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!
September 24, 2025 at 4:52 AM
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...
greglandrum.github.io/rdkit-blog/p...
Using the RDKit in a C++ program – RDKit blog
It’s actually pretty easy
greglandrum.github.io
September 20, 2025 at 2:45 AM
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...
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"
me: "Hey Siri, put onions on the shopping list"
Siri: "Ok, I put bananas on the shopping list"
September 18, 2025 at 3:42 PM
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"
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...
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
September 8, 2025 at 2:23 PM
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...
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...