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 · 12/03/2025You know how I feel about bar plots for showing distributions, right? 😀 100
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 · 25/01/2025All of it! Lots of great new datasets. More new blogs coming online with great content. Open science at its best! 110
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 · 12/12/2024Thank for the invitation @freundlichgroup.bsky.social. I had a blast! 010
Pat Walters @wpwalters.bsky.social · 11/12/2024Yes, absolutely! The approach was designed to facilitate interpretation by med chemists. 010
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 · 09/12/2024I'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. 1182
Pat Walters @wpwalters.bsky.social · 09/12/2024@prof-ajay-jain.bsky.social's response is here. www.linkedin.com/pulse/more-r...linkedin.comMore response to the response (DiffDock/DiffDock-L)To amplify on what Pat Walters said (quotes from Gabriel Corso's post in italics): It only took a few days (in August 2023) for Ann Cleves, Pat, and me to figure out that the original DiffDock work ha... 152
Pat Walters @wpwalters.bsky.social · 09/12/2024My "response to the response" is here. www.linkedin.com/pulse/my-res...linkedin.comMy Response to the ResponseResponding to our analysis, the DiffDock authors contend they were not responsible for developing the benchmark dataset or its data splits. Instead, they relied on previously published datasets and sp... 192
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 · 06/12/2024I don't know. All the DiffDock results we report are from the original DiffDock paper. 030
Pat Walters @wpwalters.bsky.social · 05/12/2024For AutoDock-Vina, we directly compared with what was in the DiffDock paper. 110
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 · 02/12/2024These 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. 010
Pat Walters @wpwalters.bsky.social · 22/11/2024I prefer to think of myself as a realistic enthusiast 😆 1140
Pat Walters @wpwalters.bsky.social · 18/11/2024What do you mean by "We should always check if the Butina split actually worked"? Do you have suggestions on better splitting approaches? 100
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
Pat Walters @wpwalters.bsky.social · 18/11/2024I do ML and put together benchmarks and guidelines for model evaluation. 240
