Martin Pacesa

Great analysis of our paper, thank you Engin!

On the lack of more biohysics: at that point it was pretty well established that these mini binders are super thermostable and highly expressed, so we chose not to include it.

Really nice, I always hated the recursive argument in transformer papers that just because you now have lower perplexity that your model is better.

Perplexity Cannot Always Tell Right from Wrong Perplexity -- a function measuring a model's overall level of "surprise" when encountering a particular output -- has gained significant traction in recent years, both as a loss function and as a simp...

Bluesky doesn’t really shine yet as a place to discover papers, especially at the intersection of biology and ML. To help a little, I’m going to start sharing papers I find interesting. To kick things off, here’s one from @petar-v.bsky.social and colleagues at DeepMind
arxiv.org/abs/2601.22950

Even project grants, which were the lifeline of many labs, are now limited…does not bode well.

🗓️ Save the Date!
The 5th European RosettaCon – Crossing Boundaries with Protein Design will take place in Lisbon, Portugal 🇵🇹
🗓️ October 28–30, 2026
Join the protein design community for an inspiring scientific meeting at the intersection of innovation and design.

Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.

Huge congratulations @nboyd.bsky.social with Mosaic that absolutely killed in the competition! 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕2 did also pretty well with the second highest hit rate in the competition!

proteinbase.com/collections/...

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org

🫨

🔬 Postdoc position – Infection Biology & Cryo-ET (Zurich) 🇨🇭
We are looking for a motivated Postdoc to join our interdisciplinary team.
📩 Interested? Check out the job advert:
www.imm.uzh.ch/dam/jcr:cb17...

👉 More info on the lab: www.weiss-laboratory.com
Please share with interested colleagues!

Shin-chaaan

Perfect birthday gift 🙌 happy this one is out!

Fully circular double rainbow appeared today while snowboarding

Super excited about our 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕 pipeline being highlighted as one of @twistbioscience.com favourite publications of 2025!

We did synthesize all binder genes with Twist ❤️

Hail the chosen one

Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏

I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful.

andrewcarroll.github.io/2025/12/23/t...

JOB ALERT: Operations Director (DCI–Lausanne).
The DCI, a joint initiative of EPFL, UNIL, UNIGE and UNIBE, is recruiting an Operations Director to lead the cryo-EM facility in Lausanne.
📩 Questions: CEO of the DCI: @chgenoud.bsky.social
🔗 Apply here: careers.epfl.ch/job/Lausanne...

Yeah, I dont think it’s a good think to show. Generating crap faster is not a bonus 😅

We could make a lot more trajectories pass if we wanted to, but we on purpose give it roadblocks along the way to make sure only very best interfaces pass. In a sense, every single hallucination iteration is a filtering step, while with diffusion you only have one step to get it right

The main difference are the self consistency steps along the way: 5 multimer models randomly swapped during design, interface must be robust enough to survive MPNN redesign, final AF2 monomer model filtering (most important), etc. Pyrosetta doesnt do much tbh

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...

This is an amazing position, DCI Lausanne is looking for a new director! It is one of the best cryoEM centers out there, with an fantastic infrastructure and some of the most exceptional experts in microscopy that I ever had the chance to work with!

careers.epfl.ch/job/Lausanne...

🚨 Today, I formally introduced articles of impeachment against Robert F. Kennedy, Jr.

RFK Jr. has turned his back on science and the safety of the American people. Michiganders cannot take another day of his chaos.

Congratulations Kiarash, that’s awesome!

Excited to share our first work on protein design! Huge thanks to the entire team, and especially to Bel, Evan, to the Doudna, Jacobsen, Cate, Banfield labs, all co-authors, and my D-lab mates! 💫

Es ist gar hübsch von einem großen Herrn,
So menschlich mit dem Teufel selbst zu sprechen.

oh, this is nice: x.com/proteinbase/.... only a few lines of code…

Submission 4 Mosaic with a Boltz2 + proteinmpnn loss. no refolding, almost no filtering and ranking ( top 20 designs by iptm -> monomer RMSD filter).

Vote for Mosaic too!
proteinbase.com/collections/...