Pat Walters
Cheminformatics, ML, Drug Discovery
- New Practical Cheminformatics Post patwalters.github.io/Three-Papers...
- New Practical Cheminformatics Post, "Useful RDKit Utils - A Mötley Collection of Helpful Routines" patwalters.github.io/Useful-RDKit...
- The latest Practical Cheminformatics post, “The Trouble With Tautomers,” emerged from a discussion about the impact of tautomers on machine learning model predictions. patwalters.github.io/The-Trouble-...
- The latest addition (#33) to the Practical Cheminformatics Tutorials series explores Bayesian optimization of reaction conditions. github.com/PatWalters/p...
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- Thanks, Colab can be picky
- 🚨 Check out DrugFlow, our new generative model for structure-based drug design. DrugFlow provides an atom-level confidence score for each designed molecule, and can adjust molecular size on the fly! Additional details in thread 🧵 #ICLR2025
- The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available 📚 Paper: openreview.net/forum?id=g3V... 💻 Code: github.com/LPDI-EPFL/Dr... (1/4)
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- You know how I feel about bar plots for showing distributions, right? 😀
- 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...
- Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...
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- All of it! Lots of great new datasets. More new blogs coming online with great content. Open science at its best!
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- Super cool!
- ChEMBL 35 is out. Happy Holidays! chembl.blogspot.com/2024/12/here...
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- Thank for the invitation @freundlichgroup.bsky.social. I had a blast!
- Excellent new paper (with code) by my former colleagues Steven Kearnes and Patrick Riley describing a procedure for associating confidence levels with regression model predictions in drug discovery. pubs.acs.org/doi/10.1021/...
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- Yes, absolutely! The approach was designed to facilitate interpretation by med chemists.
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- Well said, thank you Rommie!
- Many of you have seen Gabriele Corso's response to our recent preprint. If you haven't, it's here. www.linkedin.com/pulse/respon...
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View full thread@prof-ajay-jain.bsky.social's response is here. www.linkedin.com/pulse/more-r...
- I'm not happy with the way this all went down. I have tremendous respect for Gabriele and the rest of the DiffDock authors. Their work has broken new ground and helped advance machine learning in drug discovery. If I had to do it over again, I'd do things differently.
- My "response to the response" is here. www.linkedin.com/pulse/my-res...
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- I'm thrilled to announce a new preprint describing collaborative work with Ajay Jain and Ann Cleves Jain, "Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows". arxiv.org/abs/2412.02889
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- I don't know. All the DiffDock results we report are from the original DiffDock paper.
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- This is great, thanks for sharing
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- Point taken
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- For AutoDock-Vina, we directly compared with what was in the DiffDock paper.
- New blogpost: The ABCs of Alphafold 3, Boltz and Chai-1 blog.booleanbiotech.com/alphafold3-b...
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- These have different uses. The one liner gets the SMILES for a particular ligand. My script uses that SMILES to assign bond orders, which are missing in PDB files.
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- I prefer to think of myself as a realistic enthusiast 😆
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- Hey Polaris!
- There’s a new Practical Cheminformatics post, “Some Thoughts on Dataset Splitting,” (with code and a robot cartoon) at practicalcheminformatics.blogspot.com/2024/11/some... .
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- What do you mean by "We should always check if the Butina split actually worked"? Do you have suggestions on better splitting approaches?
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- I do ML and put together benchmarks and guidelines for model evaluation.
- Here's a Cheminformatics Starter pack! Let me know if you would like to be added! And more importantly, do encourage people to join the blue skies :Dat://did:plc:jbu62p2segkzvnuk3e4h5ga7/app.bsky.graph.starterpack/3lb4lirxegh2d
- Please add me, thanks!
- go.bsky.app/Qc4frbt Made a starter pack for computational chemists, let me know who I missed please @jchodera.bsky.social @olexandr.bsky.social @jelfschem.bsky.socialat://did:plc:no3avbdkex2mxmt4ulea5jyj/app.bsky.graph.starterpack/3laqzdsxhds2a
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- Glad to be here!
