Pat Walters @wpwalters.bsky.social · 04/09/2026M6 Mac Mini as the prize for the Marimo Cheminformatics notebook competition! 022
Pat Walters @wpwalters.bsky.social · 02/09/2026A great opportunity to showcase your marimo skills and compete for some solid prizes. Looking forward to seeing what the community builds. 010
Pat Walters @wpwalters.bsky.social · 24/08/2026Excited to team up with @marimo to explore new relationships between chemical structures and biological data. Bring your creativity, push the boundaries of reactive notebooks, and compete for prizes! Details below 👇 020
Pat Walters @wpwalters.bsky.social · 22/07/2025New Practical Cheminformatics Post patwalters.github.io/Three-Papers... 0189
Pat Walters @wpwalters.bsky.social · 13/05/2025New Practical Cheminformatics Post, "Useful RDKit Utils - A Mötley Collection of Helpful Routines" patwalters.github.io/Useful-RDKit... 071
Pat Walters @wpwalters.bsky.social · 06/05/2025The 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-...patwalters.github.ioThe Trouble With TautomersIntroductionOne factor often overlooked when applying machine learning (ML) in small-molecule drug discovery is the influence of tautomers on model predictions. Drug-like molecules, especially those c... 193
Pat Walters @wpwalters.bsky.social · 24/03/2025The latest addition (#33) to the Practical Cheminformatics Tutorials series explores Bayesian optimization of reaction conditions. github.com/PatWalters/p... 1122
Pat Walters @wpwalters.bsky.social · 10/03/2025In 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...practicalcheminformatics.blogspot.comEven More Thoughts on ML Method ComparisonsIntroduction A few things motivated this post. Some recent discussions about the virtues of LightGBM vs XGBoost Posts on TabPFN by Jon... 0339
Reposted by Pat Walterspen(Taka) @iwatobipen.bsky.social · 07/02/2025 Determine bond order from XYZ format of molecule #RDKit As readers know that recent version of RDKit supports XYZ format which is used in quantum chemistry field. The format doesn't have information of bond order. So to re-construct from the information bond order determination step is required.…iwatobipen.wordpress.com Determine bond order from XYZ format of molecule #RDKitAs readers know that recent version of RDKit supports XYZ format which is used in quantum chemistry field. The format doesn't have information of bond order. So to re-construct from the information bond order determination step is required. Recently I found useful function for determining the order in rdkit and Greg wrote useful post almost two years ago I think it's worth to read. 2132
Pat Walters @wpwalters.bsky.social · 23/01/2025Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...github.comGitHub - PatWalters/resources_2025: Machine Learning in Drug Discovery Resources 2024Machine Learning in Drug Discovery Resources 2024. Contribute to PatWalters/resources_2025 development by creating an account on GitHub. 59328
Reposted by Pat WaltersBird account @dialecticbio.bsky.social · 28/12/2024Deep learning for proteins tutorial: github.com/Graylab/DL4P...github.comGitHub - Graylab/DL4Proteins-notebooks: Colab Notebooks covering deep learning tools for biomolecular structure prediction and designColab Notebooks covering deep learning tools for biomolecular structure prediction and design - Graylab/DL4Proteins-notebooks 16828
Pat Walters @wpwalters.bsky.social · 12/12/2024ChEMBL 35 is out. Happy Holidays! chembl.blogspot.com/2024/12/here...chembl.blogspot.comHere's a nice Christmas gift - ChEMBL 35 is out!Use your well-deserved Christmas holidays to spend time with your loved ones and explore the new release of ChEMBL 35! This fresh... 0275
Pat Walters @wpwalters.bsky.social · 10/12/2024Excellent 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/...pubs.acs.orgOrdinal Confidence Level Assignments for Regression Model PredictionsWe present a simple method for assigning accurate confidence levels to molecular property predictions from regression models. These confidence levels are easy to interpret and useful for making decisi... 12611
Pat Walters @wpwalters.bsky.social · 09/12/2024Many of you have seen Gabriele Corso's response to our recent preprint. If you haven't, it's here. www.linkedin.com/pulse/respon...linkedin.comResponse to Jain et al.You may have seen a recent pre-print [1] from Jain et al. with strongly worded claims against the experimental results in our DiffDock paper [2]. 2161
Pat Walters @wpwalters.bsky.social · 05/12/2024I'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/2412.02889arxiv.orgDeep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking WorkflowsThe diffusion learning method, DiffDock, for docking small-molecule ligands into protein binding sites was recently introduced. Results included comparisons to more conventional docking approaches, wi... 109221
Pat Walters @wpwalters.bsky.social · 18/11/2024There’s a new Practical Cheminformatics post, “Some Thoughts on Dataset Splitting,” (with code and a robot cartoon) at practicalcheminformatics.blogspot.com/2024/11/some... . 46015
