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चाँद तारों को छूने की आशा... आसमानों में उड़ने की आशा...

Another AlphaFold residue-index offset hack? 🤯 But this time using it to add disulfide constraints. (neat idea to start with a simple 0,1 matrix, and then using floyd/dynamic-programming to fill in the rest of the offset matrix) biorxiv.org/content/10.110…

Well, we're packed! TIL Nathaniel and my life can be summarized by what I heard one of the movers mutter while taking down notes: "books books books books books boardgames boardgames".

Awesome thread by Pratyush Tiwary about my last first-author work as a post-doc!

We're looking for MD datasets that show protein conformational changes. All-atom or coarse grained, biased or unbiased, sidechains or loops, anything will do. What have we got?

Ooohhh I highly recommend attending Eric's talk if you can! A rare (ha ha ha) example of learning *science* with ML, not just applications thereof.

Internship opportunity at Microsoft Research #AI4Science on generative protein models. Location Berlin, Amsterdam or Cambridge. Apply here asap: jobs.careers.microsoft.com/global/en/job/…

What's a toy model for ligand binding that requires conformational change *for the ligand*?

Check out our new review led by Shams Mehdi on "Enhanced Sampling with Machine Learning" In a field that moves crazy fast, this review covers a whole lot from autoencoders to different flow models annualreviews.org/doi/abs/10.114…

We're delighted that "Protein Discovery with Discrete Walk-Jump Sampling" has won an Outstanding Paper Award at #ICLR2024! 🎉 Congratulations to Nathan C. Frey, Dan Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hötzel, Yan Wu, Stephen Ra, Richard Bonneau,

In (preemptive?) response to all the posts signaling the end of structural biology as we know it

Can we use AlphaFold2 to discover how drugs bind in specific, non-native protein conformations? Answer: no and yes. Presenting revised preprint: arxiv.org/abs/2404.07102 Gleevec is a blockbuster anti-cancer drug, having saved an estimated 350,000 lives globally since its

OpenFold developed by Gustaf Ahdritz, Nazim Bouatta, and Mohammed AlQuraishi is a trainable, open-source implementation of AlphaFold2. It is fast and memory efficient, and the code and training data are available under a permissive license. nature.com/articles/s4159…

(Please share/retweet!) Are you a Python/PyTorch expert who would like to share their love for programming with those who have never coded? For the 4th consecutive year I will be conducting summer zoom classes this July-Aug on programming in Python/Pytorch for students from

Dive into the world of explainability in graph DL for biomedicine with Chirag Agarwal and me online at #ISMB2024 on July 8! iscb.org/ismb2024/progr… 🌐💻You'll learn: 🧬 The basics of graph DL & GNNs in biomedicine 💡 Why explainability is key in biomedical ML models 🧵⬇️

Only Pratyush Tiwary could come up with this experiment! Go apply and change the paradigm of postdoctoral positions (and tell me how it goes!)