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...
Introduction A few things motivated this post. Some recent discussions about the virtues of LightGBM vs XGBoost Posts on TabPFN by Jon...
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.…
New Practical Cheminformatics Post
patwalters.github.io/Three-Papers...
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. 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.
Colab Notebooks covering deep learning tools for biomolecular structure prediction and design - Graylab/DL4Proteins-notebooks
github.com
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-...
New Practical Cheminformatics Post, "Useful RDKit Utils - A Mötley Collection of Helpful Routines"
patwalters.github.io/Useful-RDKit...
IntroductionOne 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...
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/...
The latest addition (#33) to the Practical Cheminformatics Tutorials series explores Bayesian optimization of reaction conditions.
github.com/PatWalters/p...
Pat Walters
Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...
Pat Walters
ChEMBL 35 is out. Happy Holidays!
chembl.blogspot.com/2024/12/here...
Bird account
We 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...
