You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉 Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫

Hope you all had a good summer. I'm very happy to announce the speaker line-up for the falls Chalmers AI4Science seminars! Hope to catch you all there!

If you’re interested in learning more about protein folding and misfolding, I’ve created a convenient reading list with a few essential papers: scholar.google.com/citations?us... scholar.google.com/citations?us...

1/6 One of the key features of functional proteins is their inherent structural flexibility. In our recent work at #ICML, we introduce flexibility to protein structure design! More in a thread below. Code / Tutorial: github.com/graeter-grou... Poster: W-109, Thu 17 Jul 11 a.m. PDT — 1:30 p.m. PDT

First time transatlantic and such a view over Greenland 🤯 Wish there were more glaciers :/

1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience

This is not happening, right?

New pre-print from PhD student Hang Zou on warm-starting the variational quantum eigensolver using flows: Flow-VQE! Flow-VQE is parameter transfer on steroids: it learns how to solve a family of related problems, dramatically reducing the aggregate compute cost!

Just learned that Frank Stahl (of the Meselson and Stahl DNA replication experiment ("the most beautiful experiment in biology") died at the beginning of April, to no fanfare. Here's a lovely video of them reminiscing: www.youtube.com/watch?v=7-tn...

You can now check out a recording of Julija's excellent talk on the Chalmers AI4Science YouTube channel: www.youtube.com/watch?v=y_7a...

🤹 New blog post! I write about our recent work on using hierarchical trees to enable sparse attention over irregular data (point clouds, meshes) - Erwin Transformer, accepted to ICML 2025 blog: maxxxzdn.github.io/blog/erwin/ paper: arxiv.org/abs/2502.17019 Compressed version in the thread below:

Attending conferences in Italy seems to be a great idea 🥸

I finally won a lottery and got the CA visa?! Something must be wrong.. Guess that means me + ICML 2025! 😀

Led by Fia Larsen in @rhp-lab.bsky.social, we mapped degrons in all ~1600 human transcription factors We find overlap between degrons and TADs, and show how negatively charged residues contribute to function by helping prevent degradation See preprint for much more: doi.org/10.1101/2025...

My lab, at Karolinska, in Stockholm, is looking for a PhD student with a computational/quantitative background to work on probabilistic/generative models of proteins (structure and sequence). The research will involve methods development, and applications in vaccine design.

someone said we need a meme

While this paper looks interesting, let me just say (again) that (essentially all) NMR ensembles in the PDB are NOT thermodynamic ensembles or meant to represent these. They are "uncertainty ensembles" and using them to benchmark machine learning (or other) models of dynamics is not a good idea.

A Perspective by @stephanieaw.bsky.social and @fraserlab.com discusses ways macromolecules use conformational entropy to control binding, catalysis, and allostery www.nature.com/articles/s41...

looks like it works, I was able to tariff my numpy installation: pypi.org/project/tari...

BioRxiV is very slow, so this appeared in Authorea before www.authorea.com/users/436643...

Join our efforts in biomolecular design at MPIP!

A while online now already: Predict the barrier of a reaction without knowing the transition state and in the low data regime using Gaussian Process regr. Led by Evgeni Ulanov, with Ghulam, Kai and Pascal Friederich @ KIT. @mpip-mainz.mpg.de @hitsters.bsky.social pubs.rsc.org/en/content/a...

Small proteins can be more complex than they look! We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!

Enjoyed a lot meeting all my old friends and listening to their great talks at Mosbacher Kolloquium this week! @leif-seute.bsky.social @maxfus.bsky.social

We are so excited to see where these models and data go next! 📝Paper: biorxiv.org/content/10.1... 👩‍💻Repo: github.com/WaymentSteel... 👾Colab: colab.research.google.com/github/Wayme... Huge congrats to the co-authors @hkws.bsky.social, @ramith.fyi, Hasindu, @sokrypton.org, and doro!

AI.zymes - A modular platform for evolutionary enzyme design [new] AI.zymes: Optimizes enzymes via Rosetta, ESMFold in evolution. Improves untargeted properties like electrostatic catalysis.

Mounted a co-author 😎

I'm super excited to share my recent work with @grocklin.bsky.social “Structural and energetic analysis of stabilizing indel mutations” biorxiv.org/content/10.1.... 1/8

Implicit modeling of the conformational landscape and sequence allows scoring and generation of stable proteins [new] Jointly optimizing structure & seq. improves conf. landscapes & protein designs over single objectives.

So excited to preprint this work!!

Excited about BioEmu? Opening this position for just a few days over #NeurIPS2024. Looking especially for Bioinformatics + Structural Biology skills, MD/Stat Mech skills and/or #deeplearning architecture design + engineering skills aka.ms/ai4science-r...