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Seva Viliuga

@proteinator.bsky.social
66 followers 103 following 46 posts

PhD candidate in bioinformatics Protein structure prediction / Protein design

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Reposted by Seva Viliuga
Gabriel Rocklin @grocklin.bsky.social · 19/11/2025
All data are available on Zenodo and we'd love to see what you can do with it! Cydney also made a nice notebook to run the predictive model (including DMS scan) in Colab! Preprint: biorxiv.org/content/10.1... Colab: colab.research.google.com/drive/1KNWvG... Data: docs.google.com/forms/d/e/1F...
biorxiv.org
Global Analysis of Aggregation Determinants in Small Protein Domains
Protein aggregation is an obstacle for engineering effective recombinant proteins for biotechnology and therapeutic applications. Predicting protein aggregation propensity remains challenging due to t...
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Seva Viliuga @proteinator.bsky.social · 06/01/2026
A proper way of commuting through piles of snow 🤣
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Seva Viliuga @proteinator.bsky.social · 31/12/2025
Biggest achievement of 2025 😂😂 First ever self-made cake seems to be a success!!
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/12/2025
Are you interested in integrative structural biology, but feel a bit lost? Don't worry, we have you covered with our FEBS Advanced Course, Lost in Integration Vol. 2 — probing biomolecules with AI and experiments probingbiomolecules2026.febsevents.org network.febs.org/posts/integr...
Poster for the conference
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Seva Viliuga @proteinator.bsky.social · 05/12/2025
Had a great time presenting our work on flexibility-conditioned protein structure design at @embl.org and right after our recent work on generating conformational ensembles of proteins at @euripsconf.bsky.social together with Nico. Follow along - we will be soon releasing more exciting things :)
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Simon Olsson @smnlssn.bsky.social · 10/10/2025
New preprint out! We present "Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamics,"
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025
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💫
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Simon Olsson @smnlssn.bsky.social · 25/08/2025
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!
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Reposted by Seva Viliuga
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 06/08/2025
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...
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Seva Viliuga @proteinator.bsky.social · 17/07/2025
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
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Seva Viliuga @proteinator.bsky.social · 13/07/2025
First time transatlantic and such a view over Greenland 🤯 Wish there were more glaciers :/
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The Align Foundation @alignbio.bsky.social · 08/07/2025
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
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Seva Viliuga @proteinator.bsky.social · 04/07/2025
This is not happening, right?
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Reposted by Seva Viliuga
Simon Olsson @smnlssn.bsky.social · 03/07/2025
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!
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Matthew Cobb @matthewcobb.bsky.social · 26/06/2025
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...
youtube.com
The Most Beautiful Experiment: Meselson and Stahl
YouTube video by Science Communication Lab
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Rocío Mercado Oropeza @rociomer.bsky.social · 23/06/2025
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...
youtube.com
Dr. Julija Zavadlav --- Multiscale Modeling with Machine Learning Potentials
YouTube video by Chalmers AI4Science
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Max Zhdanov @maxxxzdn.bsky.social · 21/06/2025
🤹 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:
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Seva Viliuga @proteinator.bsky.social · 15/06/2025
Attending conferences in Italy seems to be a great idea 🥸
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Seva Viliuga @proteinator.bsky.social · 29/05/2025
I finally won a lottery and got the CA visa?! Something must be wrong.. Guess that means me + ICML 2025! 😀
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/05/2025
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...
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BenjMurrell @benjmurrell.bsky.social · 15/05/2025
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.
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Gina El Nesr @ginaelnesr.bsky.social · 12/05/2025
someone said we need a meme
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 04/05/2025
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.
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Nature Chemical Biology @natchembio.nature.com · 25/04/2025
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...
nature.com
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...
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Sergey Ovchinnikov @sokrypton.org · 15/04/2025
looks like it works, I was able to tariff my numpy installation: pypi.org/project/tari...
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Reposted by Seva Viliuga
Arne Elofsson @handle.invalid · 16/04/2025
BioRxiV is very slow, so this appeared in Authorea before www.authorea.com/users/436643...
authorea.com
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...
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Seva Viliuga @proteinator.bsky.social · 05/04/2025
Join our efforts in biomolecular design at MPIP!
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Gräter lab @graeterlab.bsky.social · 31/03/2025
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...
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Gabriel Rocklin @grocklin.bsky.social · 26/03/2025
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!
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Seva Viliuga @proteinator.bsky.social · 23/03/2025
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
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Gina El Nesr @ginaelnesr.bsky.social · 20/03/2025
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!
biorxiv.org
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AI x Bio Discovery @aixbiobot.bsky.social · 22/01/2025
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.
Figure 1Figure 2Figure 3Figure 4
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Seva Viliuga @proteinator.bsky.social · 16/01/2025
Mounted a co-author 😎
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Reposted by Seva Viliuga
Yulia Gutierrez @yuliagutierrez.bsky.social · 10/01/2025
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
biorxiv.org
Structural and energetic analysis of stabilizing indel mutations
Amino acid insertions and deletions (indels) are among the most common protein mutations and necessitate changes to a protein’s backbone geometry. Examining how indels affect protein folding stability...
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Reposted by Seva Viliuga
AI x Bio Discovery @aixbiobot.bsky.social · 23/12/2024
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.
Implicit modeling of the conformational landscape and sequence allows scoring and generation of stable proteinsFigure 1Figure 2Figure 3
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Gabriel Rocklin @grocklin.bsky.social · 15/12/2024
So excited to preprint this work!!
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Frank Noe @franknoe.bsky.social · 11/12/2024
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...
aka.ms
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