The latest Practical Cheminformatics post introduces a new format, the Ranttorial™, "Comparing Classification Models - You’re Probably Doing It Wrong". practicalcheminformatics.blogspot.com/2023/11/compar…

New post at Practical Cheminformatics, “Some Thoughts on Biotech vs Pharma for Computational Chemists”. practicalcheminformatics.blogspot.com/2023/12/some-t…

The first Practical Cheminformatics post of the year is a retrospective of papers published in 2023, “AI in Drug Discovery 2023 - A Highly Opinionated Literature Review”. practicalcheminformatics.blogspot.com/2024/01/ai-in-…

Here’s the second of three posts reviewing some notable papers from 2023, “AI in Drug Discovery 2023 - A Highly Opinionated Literature Review, Part II”. practicalcheminformatics.blogspot.com/2024/01/ai-in-…

A new post at Practical Cheminformatics, "AI in Drug Discovery - A Highly Opinionated Literature Review (Part III)". Following up on parts I and II, the third post in the series is a collection of review articles published in 2023 that I found helpful. practicalcheminformatics.blogspot.com/2024/01/ai-in-…

Are you looking to start a career applying Computational Chemistry in drug discovery? I'm biased, but this is an excellent opportunity to work with a fantastic group of scientists and integrate cutting-edge experimental and computational methods. boards.greenhouse.io/relaytherapeut…

On behalf of my coauthors, I'm psyched to announce the open access publication of our paper (with code) "Thompson Sampling - An Efficient Method for Searching Ultralarge Synthesis on Demand Databases" in JCIM. pubs.acs.org/doi/10.1021/ac…

See our latest publication on RLY-4008, a highly selective irreversible small-molecule inhibitor of FGFR2, on PNASNews. Thank you to our entire team for their work on this. pnas.org/doi/10.1073/pn…

blog: calculating solvent-accessible suface area using numpy: ljmartin.github.io/blog/21_sasa_i…

I'm excited to share SyntheMol, a generative AI model for drug design optimized for creating easily synthesizable molecules. We applied our model to generate, synthesize, and validate 58 novel antibiotic candidates and found 6 potent hits. Nature Machine Intelligence nature.com/articles/s4225…

GenAI lowers the barriers to designing new chemicals. Akshay Subramanian, Wenhao Gao, Regina Barzilay, Jeff Grossman, Tommi Jaakkola, Stefanie Jegelka, Mingda Li, Ju Li, Wojciech Matusik, Elsa Olivetti, Connor W. Coley & RGB Lab @ MIT discuss opportunities and risks: mit-genai.pubpub.org/pub/681kpeoa/r…

Looking forward to your contributions to the new themed article collection (TAC) on “Good Practices in AI” sciencedirect.com/journal/artifi…

I've added 3 new Active Learning tutorials to the Practical Cheminformatics Tutorial series, bringing the total number of tutorials to 24. github.com/PatWalters/pra…

I've added four new tutorials to the "Fundamentals" section of "Practical Cheminformatics Tutorials", bringing the total number of Jupyter notebooks to 28. All the tutorials can be run on Google Colab without installing any software locally. github.com/PatWalters/pra…

New Practical Cheminformatics Post, "Generative Molecular Design Isn't As Easy As People Make It Look", practicalcheminformatics.blogspot.com/2024/05/genera…

Great post on AlphaFold3 from Inductive Bio that I'm surprised has not got more attention🤔 - AF3 paper benchmarked Vina (not SOTA) using a single conf - Conventional docking has near AF3 performance when using multiple starting confs and Gnina scoring to select best pose (1/2)

🚀 Excited to announce that "Bayesian Illumination: Inference and Quality-Diversity Accelerate Generative Molecular Models" is now available! Key takeaway: Bayesian Illumination is 100x more effective than either genetic algorithms or deep generative models. 📊

As someone who has spent a lot of time writing, talking, and complaining about the sad state of benchmarks in our field, I'm incredibly excited by the Polaris platform. This effort will enable the community to easily share datasets and best practices for ML model validation.

New Practical Cheminformatics Tutorial, “Analyzing Patent Data from BindingDB”. colab.research.google.com/github/PatWalt…

Thrilled to announce a preprint describing collaborative work between our group and James Fraser (A$AP J), Brian Shoichet, and Adam Renslo. The paper shows a practical application of the Thompson Sampling method we published earlier this year. biorxiv.org/content/10.110…