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Seva Viliuga

@proteinator.bsky.social

59 followers 96 following 40 posts

PhD candidate in bioinformatics Protein structure prediction / Protein design

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Seva Viliuga @proteinator.bsky.social · Jul 17

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

Seva Viliuga @proteinator.bsky.social · 20d

FAMPNN or PPIpack?

github.com/richardshuai...

colab.research.google.com/github/Kuhlm...

GitHub - richardshuai/fampnn: Sidechain conditioning and modeling for full-atom protein sequence design

Sidechain conditioning and modeling for full-atom protein sequence design - richardshuai/fampnn

Reposted by Seva Viliuga

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 26d

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💫

Seva Viliuga @proteinator.bsky.social · Aug 27

Good luck and enjoy, Seb!

Reposted by Seva Viliuga

Simon Olsson @smnlssn.bsky.social · Aug 25

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!

Reposted by Seva Viliuga

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Aug 6

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...

Seva Viliuga @proteinator.bsky.social · Jul 17

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!

Seva Viliuga @proteinator.bsky.social · Jul 17

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.

Seva Viliuga @proteinator.bsky.social · Jul 17

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.

Seva Viliuga @proteinator.bsky.social · Jul 17

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.

Seva Viliuga @proteinator.bsky.social · Jul 17

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.

Seva Viliuga @proteinator.bsky.social · Jul 17

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

Seva Viliuga @proteinator.bsky.social · Jul 13

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

Seva Viliuga @proteinator.bsky.social · Jul 13

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

Reposted by Seva Viliuga

The Align Foundation @alignbio.bsky.social · Jul 8

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

Seva Viliuga @proteinator.bsky.social · Jul 4

This is not happening, right?

Javi Ibarrondo @jibarrondo.bsky.social · Jul 3

Exclusive: Famed protein structure competition nears end as NIH grant money runs out | Science | AAAS www.science.org/content/arti... 🧪

Exclusive: Famed protein structure competition nears end as NIH grant money runs out

Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold

www.science.org

Reposted by Seva Viliuga

Simon Olsson @smnlssn.bsky.social · Jul 3

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!

Seva Viliuga @proteinator.bsky.social · Jun 27

"...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...

Seva Viliuga @proteinator.bsky.social · Jun 26

🫠

Reposted by Seva Viliuga

Matthew Cobb @matthewcobb.bsky.social · Jun 26

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...

The Most Beautiful Experiment: Meselson and Stahl

YouTube video by Science Communication Lab

www.youtube.com

Reposted by Seva Viliuga

Rocío Mercado Oropeza @rociomer.bsky.social · Jun 23

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...

Reposted by Seva Viliuga

Max Zhdanov @maxxxzdn.bsky.social · Jun 21

🤹 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:

Seva Viliuga @proteinator.bsky.social · Jun 15

Attending conferences in Italy seems to be a great idea 🥸

Seva Viliuga @proteinator.bsky.social · May 29

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

Reposted by Seva Viliuga

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · May 18

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...

Reposted by Seva Viliuga

BenjMurrell @benjmurrell.bsky.social · May 15

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.