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proteinator.bsky.social
PhD candidate in bioinformatics Protein structure prediction / Protein design
28 posts 39 followers 83 following
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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...

submitted 15 hours ago • 5 comments

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...

submitted 3 days ago • 0 comments

🤹 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:

submitted 5 days ago • 1 comment

Attending conferences in Italy seems to be a great idea 🥸

submitted 11 days ago • 0 comments

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

submitted 28 days ago • 0 comments

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...

submitted 39 days ago • 1 comment

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.

submitted 42 days ago • 2 comments

someone said we need a meme

submitted 45 days ago • 1 comment

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.

submitted 53 days ago • 9 comments

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...

submitted 62 days ago • 0 comments

looks like it works, I was able to tariff my numpy installation: pypi.org/project/tari...

submitted 72 days ago • 0 comments

BioRxiV is very slow, so this appeared in Authorea before www.authorea.com/users/436643...

submitted 71 days ago • 1 comment

Join our efforts in biomolecular design at MPIP!

submitted 82 days ago • 0 comments

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...

submitted 87 days ago • 0 comments

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!

submitted 92 days ago • 4 comments

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

submitted 96 days ago • 0 comments

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.

submitted 155 days ago • 0 comments

Mounted a co-author 😎

submitted 161 days ago • 0 comments

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

submitted 167 days ago • 1 comment

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.

submitted 185 days ago • 0 comments

So excited to preprint this work!!

submitted 193 days ago • 3 comments

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...

submitted 197 days ago • 0 comments