Change heterocycle to another isoster with HCIE #memo #cheminformatics #RDKit iwatobipen.wordpress.com/2026/03/08/c...
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#rdkit
Latest posts tagged with #rdkit on Bluesky
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Posts tagged #rdkit
The new #RDKit blog post is a guest post looking at doing Butina clustering on the GPU using nvMolKit.
greglandrum.github.io/rdkit-blog/p...
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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…
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In this week's #RDKit blog post I assemble a new data set of compounds from patents.
greglandrum.github.io/rdkit-blog/p...
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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…
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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…
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The last #RDKit blog post of the year is a brief look back at 2025.
greglandrum.github.io/rdkit-blog/p...
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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...
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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...
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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...
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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…
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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...
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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...
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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…
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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...
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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...
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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…
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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...
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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.
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The new #RDKit blog post shows off some reaction drawing tricks.
greglandrum.github.io/rdkit-blog/p...
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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...
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A screenshot showing that my "rdkit_new" conda environment is running the 2025.09.1 RDKit release
Yay! #RDKit
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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…
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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...
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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...
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GitHub - NVIDIA-Digital-Bio/nvMolKit: A high-performance, GPU-accelerated library for key computational chemistry tasks, such as molecular similarity, conf... #nvidia #nvmolkit #molecularmodeling #compchem #morgan #fingerprints #tanimoto #mmff #rdkit #gpu #conformergeneration #minimization
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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…
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Thanks to @greglandrum.bsky.social and all the #RDKit crew another great UGM,now back along the Elbe as the sun sets:
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