Manas Mahale

This Week In Cheminformatics Issue #011 is out.

This week we look into Model for Pure Shift Proton NMR, Uncertainty Quantification, What Happens in Successful Optimizations and a long list of papers. Happy reading :)

thisweekincheminformatics.substack.com/p/eleven

This Week In Cheminformatics Issue #010 is out.

This week we look into Novel NP Inspired Chemotypes for Kinase, Virtual Screening with GPU using UniDock-Pro, Benchmarking Count Fingerprint Performance and a Long List of Papers. Happy reading :)

thisweekincheminformatics.substack.com/p/ten

This Week In Cheminformatics Issue #009 is out.

This week we look into New Ligand Target Prediction Models, Rules on model validation and a long list of papers. Happy reading :)

thisweekincheminformatics.substack.com/p/nine

This Week In Cheminformatics Issue #008 is out.

This week we look into Weighted fingerprints, curated annotation of ChEMBL, a compound prioritization method and a long list of papers from last week. Happy reading :)

thisweekincheminformatics.substack.com/p/eight

This Week In Cheminformatics Issue #007 is out.

This week we look into an intuitive method for improving reaction coverage in USPTO, Massive Crystal structure data release from FAIR and a Long list of papers. Happy reading :)

thisweekincheminformatics.substack.com/p/seven

This week we look into Binding Site Vectors to Compare Active Sites, ArtiDock, Benchmarking Boltz-2, and a long list of papers from last week of Jan.

This Week In Cheminformatics Issue #006 is out.

This week we look into Binding Site Vectors to Compare Active Sites, ArtiDock, Benchmarking Boltz-2, and a long list of papers from last week of Jan. Happy reading :)

thisweekincheminformatics.substack.com/p/six

Tomorrow in the reading group we discuss "SeedFold: Scaling Biomolecular Structure Prediction" arxiv.org/abs/2512.24354

Outperforming AF3 on multiple tasks a little bit.

Join us on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/starklyspeak...

This Week In Cheminformatics: Issue #005 CACHE Challenge #3, Digital pipette, Bias in retrosynthesis datasets, Benchmarking self-driving labs and a long list of papers to start the final week of January.

This Week In Cheminformatics Issue #005 is out.

thisweekincheminformatics.substack.com/p/five

This Week In Cheminformatics: Issue #003 Better Ensemble For Federated Learning, A New Chirality, Transformer Model's Memorization Limiting Performance, Closed-Loop Molecular Discovery and Results of Blind Challenge on Pan-Coronavirus Data

This Week In Cheminformatics Issue #003 is out.

thisweekincheminformatics.substack.com/p/three

This Week In Cheminformatics: Issue #002 First week's readings, Big W for OpenFE, Andrew Dalke and RNA Structure Prediction

This Week In Cheminformatics, we look into massive validation study from Open Free Energy, Andrew Dalke’s clever method for preserving count magnitudes in binary fingerprints and results of Stanford Kaggle competition for RNA structure prediction.

thisweekincheminformatics.substack.com/p/two

literally no one asked, but I started a newsletter.
it’s called "This Week In Cheminformatics" (very original, I know). First issue is out now.
have a read and a very happy new year !

thisweekincheminformatics.substack.com/p/one

#cheminformatics

Manas Mahale

manasmahale.in/essay/moj

It’s an interactive explorer for More O’Ferrall-Jencks diagrams. You can visualize the transition state shifting in real-time (unlike my grade, which is now fixed in stone :p ).

If you have an exam coming up soon, this is for you. If you already finished yours. well, come share my pain.

#chemistry

More on More O'Ferrall-Jencks Diagram Surfing the Potential Energy Surface

I sat for my Physical Organic Chemistry exam 48 hours ago.

Naturally, immediately after the exam, my brain finally decided to better understand the material. So, to cope with the irony, I spent my weekend building this.

butwhyisthat.substack.com/p/moj

Enjoyed reading

“AI for chemistry in 2025 is like AI for images in 2010”

leashbio.substack.com/p/ai-for-che...

Rafa has come out swinging this morning 😂

GitHub - Manas02/Tanki: Terminal Based SRS Terminal Based SRS. Contribute to Manas02/Tanki development by creating an account on GitHub.

I made a Terminal based Anki clone (Spaced Repetition System TUI) for no reason !

github.com/Manas02/Tanki

It’s surprising how much you can do without JS

manasmahale.in/resume.html

This is what happens when you let computer scientists design molecules 🤯 Oral presentation @neuripsconf.bsky.social #NeurIPS2024 #chemsky

I am speaking at CPHI Middle East in Riyadh this week, on

"Artificial Intelligence Across Modalities - Small Molecules, Antibodies/Proteins, and Cell and Gene Therapy"

Please don't hesitate to get in touch if you are interested in AI & drug discovery! Cheers, Andreas

www.cphi.com/middle-east/...

PKSmart v3.0 is now live! pk-predictor.serve.scilifelab.se

PKSmart is an open-source app we built to predict human and animal pharmacokinetic parameters. Publication is coming soon and is also available for local implementation via pip install pksmart.

pksmart PKSmart: An Open-Source Computational Model to Predict in vivo Pharmacokinetics of Small Molecules

pip install pksmart

pypi.org/project/pksm...

Out-of-Distribution Validation for Bioactivity Prediction in Drug... Recent advances in machine learning for materials science have significantly improved the prediction of novel materials. Building on these methods, we have adapted them for drug discovery...

We translated a validation strategy in Materials to Small molecules.

A key problem in cross-validation is splitting of data. Here we propose a step-forward CV. People are used to scaffold splits, time splits etc. but these all have limitations.

Extended Activity Cliffs‐Driven Approaches on Data Splitting for the Study of Bioactivity Machine Learning Predictions The presence of Activity Cliffs (ACs) has been known to represent a challenge for QSAR modeling. With its high data dependency, Machine Learning QSAR models will be directly influenced by the activit...

About activity cliffs, sampling, similarity, and ML training:
onlinelibrary.wiley.com/doi/10.1002/...

✋

Great to see the communities re-forming!

Lately, on the side closer to cheminformatics, I've looked at the limits of predictive power of machine learning models

A cartoon robot using a chainsaw on a log

There’s a new Practical Cheminformatics post, “Some Thoughts on Dataset Splitting,” (with code and a robot cartoon) at practicalcheminformatics.blogspot.com/2024/11/some... .

related, this wonderful post by @greglandrum.bsky.social

greglandrum.github.io/rdkit-blog/p...

Yes, I began collecting various implementations of scaffold split, and there’s quite a variety of them. In general, your point that the scaffold split essentially resembles random sampling except in cases with clearly clustered data holds true when we examine those implementations.

GitHub - dehaenw/world-s-simplest-ECFP: the world's simplest ECFP the world's simplest ECFP. Contribute to dehaenw/world-s-simplest-ECFP development by creating an account on GitHub.

The world's simplest ECFP implementation: github.com/dehaenw/worl... #chemsky #cheminformatics

GitHub - Manas02/analogue-split: pip install analoguesplit pip install analoguesplit. Contribute to Manas02/analogue-split development by creating an account on GitHub.

Analogue Split creates train-test sets with a fraction (γ) of activity cliffs—molecular pairs with high similarity (above a threshold, ω) but with different activity labels. Results are visualized for metrics like accuracy, precision, recall, and F1-score across γ.

github.com/Manas02/anal...