@JCIM_JCTC @sgj30 @songyojung @Cambridge_Uni @JCIM_JCTC It's distressing that authors continue to publish papers using the highly flawed MoleculeNet dataset. Journals like @JCIM_JCTC must provide guidelines on what constitutes an acceptable validation.

@Azhar__Shaikh Given my chemistry background, I have my own biases, but I believe that domain knowledge is essential for anyone involved in ML for drug discovery.

ChEMBL 35 is out. Happy Holidays!

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.

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.

@DdelAlamo @prof_ajay_jain Time splits with the pdb are a profoundly bad idea. Groups often deposit a novel structure and then deposit the structures of analogs a couple of years later. Efforts like Plinder are addressing this.

There’s a new Practical Cheminformatics post, “Some Thoughts on Dataset Splitting,” (with code and a robot cartoon) at

RT @Polaris_HQ: Introducing our first proposed set of guidelines for method comparison in small molecule property prediction! Crafted by t…

RT @Polaris_HQ: Excited to introduce the first steering committee (SC) from Polaris! This group of industry experts is focused on small-mol…

There’s a new Practical Cheminformatics blog post, “Silly Things Large Language Models Do With Molecules.” In this post, I explain why general-purpose LLMs aren’t appropriate for analog generation and suggest better alternatives.

Thanks to everyone who attended the AI in Drug Discovery Workshop at the RSC 7th Symposium on AI in Chemistry.  We’ve made the materials (slides, Jupyter notebooks, resource list) from the three hour workshop available on GitHub.  #AIChem24

@rguha @RommieAmaro @MatthiasRarey @ACSCINF Congrats, Rajarshi!

RT @BiologyAIDaily: BindingDB in 2024: a FAIR Knowledgebase of Protein-Small Molecule Binding Data - This paper provides an update on Bind…

Thrilled to announce a preprint describing collaborative work between our group and @fraser_lab, @BShoichet, and @adamrenslo. The paper shows a practical application of the Thompson Sampling method we published earlier this year.

New Practical Cheminformatics Tutorial, “Analyzing Patent Data from BindingDB”.