Seva Viliuga
@proteinator.bsky.social
PhD candidate in bioinformatics
Protein structure prediction / Protein design
Protein structure prediction / Protein design
Pinned
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
Code / Tutorial: github.com/graeter-grou...
Poster: W-109, Thu 17 Jul 11 a.m. PDT — 1:30 p.m. PDT
Reposted by Seva Viliuga
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💫
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
September 12, 2025 at 12:43 PM
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💫
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
Reposted by Seva Viliuga
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!
August 25, 2025 at 10:41 AM
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
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...
scholar.google.com/citations?us...
scholar.google.com/citations?us...
August 6, 2025 at 7:01 PM
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...
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
Code / Tutorial: github.com/graeter-grou...
Poster: W-109, Thu 17 Jul 11 a.m. PDT — 1:30 p.m. PDT
July 17, 2025 at 4:19 AM
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
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 :/
July 13, 2025 at 9:57 PM
First time transatlantic and such a view over Greenland 🤯 Wish there were more glaciers :/
Reposted by Seva Viliuga
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
🚀 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
July 8, 2025 at 4:26 PM
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
🚀 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?
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
July 4, 2025 at 7:10 AM
This is not happening, right?
Reposted by Seva Viliuga
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!
July 3, 2025 at 8:18 AM
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!
Reposted by Seva Viliuga
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
June 26, 2025 at 10:01 AM
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...
Reposted by Seva Viliuga
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...
June 23, 2025 at 7:03 AM
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
🤹 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:
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:
June 21, 2025 at 4:23 PM
🤹 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:
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 🥸
June 15, 2025 at 9:37 PM
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! 😀
May 29, 2025 at 4:02 PM
I finally won a lottery and got the CA visa?! Something must be wrong.. Guess that means me + ICML 2025! 😀
Reposted by Seva Viliuga
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...
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...
May 18, 2025 at 8:57 AM
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...
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
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.
May 15, 2025 at 1:21 PM
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.
Reposted by Seva Viliuga
someone said we need a meme
May 12, 2025 at 3:35 PM
someone said we need a meme
Reposted by Seva Viliuga
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.
May 4, 2025 at 2:58 PM
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.
Reposted by Seva Viliuga
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...
www.nature.com/articles/s41...
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...
www.nature.com
April 25, 2025 at 3:35 PM
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...
www.nature.com/articles/s41...
Reposted by Seva Viliuga
looks like it works, I was able to tariff my numpy installation:
pypi.org/project/tari...
pypi.org/project/tari...
April 15, 2025 at 7:48 PM
looks like it works, I was able to tariff my numpy installation:
pypi.org/project/tari...
pypi.org/project/tari...
Reposted by Seva Viliuga
BioRxiV is very slow, so this appeared in Authorea before www.authorea.com/users/436643...
AlphaFold3 at CASP16
The CASP16 experiment provided the first opportunity to benchmark AlphaFold3. In contrast to AlphaFold2, AlphaFold3 can predict the structure of non-protein molecules, and according to the benchmark p...
www.authorea.com
April 16, 2025 at 9:44 AM
BioRxiV is very slow, so this appeared in Authorea before www.authorea.com/users/436643...
Join our efforts in biomolecular design at MPIP!
Job alert: Join us in Mainz as
Max Planck Research Group Leader (W2) in Molecular Design
...and make your own research dreams happen on de novo design, generative models, proteins, materials ...
tinyurl.com/r2xjxnuk
@mpip-mainz.mpg.de
Max Planck Research Group Leader (W2) in Molecular Design
...and make your own research dreams happen on de novo design, generative models, proteins, materials ...
tinyurl.com/r2xjxnuk
@mpip-mainz.mpg.de
Max Planck Research Group Leader (W2) in Molecular Design
We are looking for exceptional early-career scientists conducting computational research with a proven record of accomplishment. The primary focus of this call is on candidates proposing research on b...
tinyurl.com
April 5, 2025 at 8:34 AM
Join our efforts in biomolecular design at MPIP!
Reposted by Seva Viliuga
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...
Led by Evgeni Ulanov, with Ghulam, Kai and Pascal Friederich @ KIT.
@mpip-mainz.mpg.de @hitsters.bsky.social
pubs.rsc.org/en/content/a...
March 31, 2025 at 12:04 PM
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...
Led by Evgeni Ulanov, with Ghulam, Kai and Pascal Friederich @ KIT.
@mpip-mainz.mpg.de @hitsters.bsky.social
pubs.rsc.org/en/content/a...
Reposted by Seva Viliuga
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!
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!
March 26, 2025 at 4:21 PM
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!
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
@leif-seute.bsky.social @maxfus.bsky.social
March 23, 2025 at 12:00 AM
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
@leif-seute.bsky.social @maxfus.bsky.social
Reposted by Seva Viliuga
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!
📝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!
biorxiv.org
March 20, 2025 at 7:13 PM
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!
📝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!