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...

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...

biorxiv.org

A proper way of commuting through piles of snow 🤣

Biggest achievement of 2025 😂😂 First ever self-made cake seems to be a success!!

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...

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.

I attended a summer school on Spetses 🇬🇷 just as I was beginning my PhD. Looks like I will be going again in 2026 with "Lost in Integration vol. 2". Details to follow.

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 :)

New preprint out! We present "Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamics,"

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?

Javi Ibarrondo@jibarrondo.bsky.social · last yr.

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

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...

The Most Beautiful Experiment: Meselson and Stahl

YouTube video by Science Communication Lab

youtube.com

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...

Dr. Julija Zavadlav --- Multiscale Modeling with Machine Learning Potentials

YouTube video by Chalmers AI4Science

youtube.com

Simon Olsson@smnlssn.bsky.social · last yr.

Today we are excited to welcome Julija Zavadlav (TUM) the the spring terms final instance of the Chalmers AI4Science seminar series. You can join us in person in Analysen (EDIT building) or via zoom check details here: psolsson.github.io/AI4ScienceSe...

🤹 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...

Rasmus Hartmann-Petersen@rhp-lab.bsky.social · last yr.

With the @lindorfflarsen.bsky.social group we present our map of degrons in all human transcription factors, incl. examples of constitutive degrons in exposed regions & buried degrons that are exposed upon mutation. In addition, we show that most TADs overlap with degrons. Work led by Fia Larsen.

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

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · 2y ago

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.

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.

bioRxivpreprint@biorxivpreprint.bsky.social · 2y ago

Towards Unraveling Biomolecular Conformational Landscapes with a Generative Foundation Model https://www.biorxiv.org/content/10.1101/2025.05.01.651643v1

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...

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...

nature.com

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!

Gräter lab @graeterlab.bsky.social · 2y ago

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

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