Seva Viliuga

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...

6/6 Amazing team work with great co-authors
@leif-seute.bsky.social, Nicolas Wolf, Simon Wagner, @bioinfo.se, Jan Stühmer and @graeterlab.bsky.social

Try out FliPS and BackFlip yourself, code and Google Colab tutorials are available on GitHub!

5/6 We introduce a framework in which we generate candidate protein structures conditioned on flexibility with FliPS and use BackFlip to select the candidates whose predicted flexibility profile best matches the target before running expensive MD simulations.

4/6 We also introduce BackFlip - an equivariant network that can accurately predict backbone flexibility as derived from MD simulations. Crucially, BackFlip infers flexibility solely from the backbone geometry without requiring evolutionary information, making it useful for de novo protein design.

3/6 In a series of experiments, we demonstrate that FliPS samples novel, realistic proteins with diverse secondary structure composition and a remarkable resemblance to custom target flexibility profiles, as verified in 300ns Molecular Dynamics (MD) simulations of the designed samples.

2/6 Our model FliPS is a conditional flow matching model for protein structure generation. FliPS receives a flexibility profile as conditional input feature and learns how to generate realistic protein structures while respecting target flexibilities.

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 :/

Hahaha this is hilarious!! I’m now totally convinced I should play with it as well 🤣

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!

"...we investigated the performance of ... inverse folding models when trained on different structural datasets and on held-out set of experimentally determined PDB structures."

It would be interesting if they did it vice versa and ran inference on some FoldSeek or dark clusters of AFDB...

🫠

YouTube video by Science Communication Lab The Most Beautiful Experiment: Meselson and Stahl

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.

precious!

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.

Is there a stream of the talk or maybe there’s gonna be a recording?

Not sure it’s so trivial 😅 ENM assumes a harmonic potential, which by definition limits the exploration of states far from equilibrium state. If pico-(low)nanosecond dynamics is of interest, maybe it can be considered trivial; is it anyhow informative - is another question..

Advances in uncovering the mechanisms of macromolecular conformational entropy - Nature Chemical Biology Protein conformational entropy plays a vital role in functions like binding and catalysis. This Perspective discusses three ways macromolecules use conformational entropy: prepaying entropic costs, re...

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...

Nice! Looking forward 🥸

I think the more interesting msg is that one doesn’t gain a lot by scaling up the datasets contrasting to what still seems to be quite a consensus in the pLMs field… 😅