Excited to share our now published paper @cp-cell.bsky.social highlighting advances in modeling the evolution of protein-protein interactions with MSA Pairformer. Big thanks to Zhidian Zhang, Olivia Tang, @eunbelivable.bsky.social @milot.bsky.social @martinsteinegger.bsky.social and @sokrypton.org!

Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer

Protein language models have excelled at modeling individual proteins, but extending these capabilities to protein complexes remains a major challenge. MSA Pairformer, a parameter-efficient protein la...

cell.com

Atomic models powered bioAI's first era. Experiments measure more. @rs-station.bsky.social is joining omsf.io to unlock interpretation of raw exp observables at scale (blog👇); we'll partner with @openfold.io, @openbind.bsky.social , and cryo-EM+X-ray facilities to make this routine. Join us!

Reciprocal Space Station@rs-station.bsky.social · last mo.

1/ We're excited to announce that @rs-station.bsky.social is joining the Open Molecular Software Foundation @omsf.io!

We are implementing a similar policy at @arxiv.bsky.social. If there is incontrovertible evidence of LLM slop in a paper, this means the authors did not take the time to read the LLM output and we can't trust anything else in the paper. Penalty is 1 year ban from arXiv followed by...

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15

AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network

Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...

rdcu.be

I'm excited to announce some major updates to our ProteinEBM paper with Chenxi Ou @sokrypton.org!

New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

On the nature of the earliest known lifeforms

On the nature of the earliest known lifeforms

Microfossils reported from Archaean BIFs most likely were liposome-like protocells, which had evolved intracellular mechanisms for energy conservation but not for regulating cell morphology and replication.

buff.ly

Five years ago, we released FLIP. The core question was: can ML models for protein fitness prediction generalize in the ways that actually matter for protein engineering, i.e. low data, extrapolation to more mutations, out-of-distribution sequences?

New pre-print from the lab on scaling transferable implicit transfer operators to protein dynamics. Collaboration with @olewinther.bsky.social lead by @panosantoniadis.bsky.social.

Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure. We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)

While most AI models are trained on text and images, the Polymathic AI collaboration has something different in mind: AI trained on #physics: https://www.simonsfoundation.org/2025/12/09/these-new-ai-models-are-trained-on-physics-not-words-and-theyre-driving-discovery/ #science

These New AI Models Are Trained on Physics, Not Words, and They’re Driving Discovery

These New AI Models Are Trained on Physics, Not Words, and They’re Driving Discovery on Simons Foundation

simonsfoundation.org

New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! www.biorxiv.org/content/10.6...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...

Multiple protein structure alignment at scale with FoldMason

Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

science.org

Important perspective from Greenland.

UK Research and Innovation, plus its research councils, quietly quit X. Via @robinbisson.bsky.social @sophieatrpn.bsky.social www.researchprofessionalnews.com/rr-news-uk-r...

UK Research and Innovation and its councils quietly quit X - Research Professional News

Funding agency has “been using alternative platforms” amid ongoing controversies over social media company

researchprofessionalnews.com

I found the secret Pret at Heathrow Terminal 5

This was fun work and a remarkable effort across the computational and wet-lab teams! Strategies for in-silico filtering and ranking of antibody designs have been under-discussed in the literature, e.g. in most technical reports on antibody design that I've seen. Let's talk about these here! [1/n]

AI x Bio Discovery@aixbiobot.bsky.social · 7mo ago

Origin-1: a generative AI platform for de novo antibody design against novel epitopes [new] GenAI designs novel Ab targeting. It uses structure, sequence, & co-folding for binding.

At Absci, we performed de novo antibody design campaigns against "zero-prior" epitopes—lacking structural data from antibody-antigen or protein-protein complexes. Model architectures, training data curation, and scoring protocols are fully described. Preprint: www.absci.com/wp-content/u...

fine.house.gov/news/documen...

Congressman Fine Introduces Greenland Annexation and Statehood Act to Strengthen U.S. National Security and Put Our Adversaries on Notice

Today, Congressman Fine (FL-06) introduced the Greenland Annexation and Statehood Act, landmark legislation focused on securing America’s strategic national security interests in the Arctic and counte...

fine.house.gov

GERMAN PRESIDENT STEINMEIER: “.. the United States has broken with the values that it helped to establish .. “.. we have now moved beyond the stage where we can lament the lack of respect for international law or the erosion of the international order; we are far beyond that, I believe.”

Recently found out about @jvkersch.bsky.social's `tmtools` github.com/jvkersch/tmt.... It works nicely! Being able to pass user-defined sequence alignments is a nice (if simple) feature that is missing from OpenStructure's own `tmtools` @torstenschwede.bsky.social.

Black swan moment for energy production and storage?

🏛️ 🔍 👀 "There are no optical corrections in the Parthenon"

Alain Goriely@alaingoriely.bsky.social · 10mo ago

The illusion of illusions One of the oldest myths in human history is that the Parthenon was cleverly built with curves so that it looks straight, to correct some visual illusions In this paper I demonstrate that there are NO optical corrections in the Parthenon arxiv.org/abs/2510.16831. [1/n]

Visiting Ephesus at #embointegmod25 to look for the missing AlphaFold 3 code

Would you like to come to my lab for a postdoctoral position? Apply for the EPFL AI Centre fellowship: epfl.ch/research/fun.... FYI, I have funding (ERC & Simon's collaboration) also for 1-2 top candidates who will not secure the fellowship. Same for @krzakalaf.bsky.social lab.

EPFL AI Center and Swiss AI Initiative Postdoctoral Fellowships

The 2nd call is now open with a deadline for submissions of 3 November (17.00 CET)!Applications are encouraged from researchers at the postdoctoral level with a keen interest in collaborative, interdi...

epfl.ch

💥 We are *also* organizing Machine Learning for Structural Biology @ EurIPS, Copenhagen!! Topics include anything in the ML+bio intersection. Submit your ML+bio short papers! Authors can even present in both locations if they have people in both locations 🚀

MLSB (in San Diego + Copenhagen)@workshopmlsb.bsky.social · 12mo ago

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💫

Cool-looking work by @piompons.bsky.social @albecazzaniga.bsky.social @fra-cutu.bsky.social, going beyond existing works on sampling different conformational ensembles with AF2.

Valerio Piomponi@piompons.bsky.social · 12mo ago

Our study is now published on JCIM🎉 We expanded and refined the preprint thanks to the insightful feedback from reviewers! paper: pubs.acs.org/doi/10.1021/... code: github.com/RitAreaScien...

Posts about research on Bluesky receive substantially more attention than similar posts on X, formerly called Twitter go.nature.com/45Ftiw4

Research posts on Bluesky are more original — and get better engagement

Bluesky posts about science garner more likes and reposts than similar ones on X.

go.nature.com