We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale See preprint for: — Ensembles of >12000 full-length human proteins — Analysis of IDRs in >1500 TFs 📜 doi.org/10.1101/2025... 💾 github.com/KULL-Centre/...

We have a job opening at Peptone.io for an ML researcher. Come help us find new ways to understand and drug intrinsically disordered proteins (IDPs), it's a very interesting and important problem! Link in the reply ↓

Very interesting and powerful method! www.nature.com/articles/s43...

The plan at FutureHouse has been to build scientific agents for discoveries. We’ve spent the last year researching the best way to make agents. We’ve made a ton of progress and now we’ve engineered them to be used at scale, by anyone. Free and on API.

Presenting one of my favorite manuscripts I've ever worked on: "Characterizing structural and kinetic ensembles of intrinsically disordered proteins using writhe" www.biorxiv.org/content/10.1... by Tommy Sisk, with a generative modeling component done in collaboration with @smnlssn.bsky.social

"De novo prediction of protein structural dynamics" I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...

Presenting our work on minimum energy path generation between two states for physical systems at the FPI Workshop at @ICLR tomorrow! Scaling up to solvated BPTI and observing the same conformational changes as long reference MD with six orders fewer force field evals! Drop by!

New preprint on arXiv! We propose a new technique to compute kinetic rates using multiple independent non-equilibrium (ratchet&pawl MD) simulations! We focused here on ligand unbinding kinetics, but this method can be applied to any situation where a reaction coordinate can be defined!

AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...

BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design by @yehlincho.bsky.social @martinpacesa.bsky.social @sokrypton.org 🧶🧬 www.biorxiv.org/content/10.1...

Wondering how to predict protein flexibility in a sec? No time to run MD simulations but want to go beyond pLDDT? Check out BBFlow arxiv.org/html/2503.05... Useful in particular for de novo designs. Led by Nico Wolf & Leif Seute, w Seva, Simon, and Jan. @mpip-mainz.mpg.de @hitsters.bsky.social

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!

Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics? @hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1! 🧵

Straight to the reading list: Training a machine learning model based on residues with missing NMR assignments as a proxy for protein motion

Very excited for my first BSKY post. We present a new method, Loxodynamics, for exploring chemical and catalytic reaction space!

Our review on machine learning methods to study sequence–ensemble–function relationships in disordered proteins is now out in COSB authors.elsevier.com/sd/article/S... Led by @sobuelow.bsky.social and Giulio Tesei

The paper describing our community effort to collect and organize #plumed tutorials has been published in the Journal of Chemical Physics, as part of the Michele Parrinello Festschrift! doi.org/10.1063/5.02...

As a peek toward where we're headed: Right now, CADD scientists are forced to use the same model week after week, even if new experimental data says the model is inaccurate. If we can fine- models, we can exploit that data to systematically improve our predictions week by week!

The BioEmu-1 model and inference code are now public under MIT license!!! Please go ahead, play with it and let us know if there are issues. github.com/microsoft/bi...

I am hiring a postdoctoral scholar with a start date summer or fall 2025. Projects will be focused on thermodynamically consistent generative models, broadly defined. If you’re interested, please send a CV and one paragraph about why you think you’d be a good fit to [email protected]

It’s been 20 years today since my first paper on intrinsically disordered proteins Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations doi.org/10.1021/ja04... and I thought I would tell the somewhat random path that led to this paper. 1/n

With today's report outlining risks on mirror life www.science.org/doi/full/10.... many have asked: Could mirror life survive in the wild? Yes. While mirror life in the wild could have some significant disadvantages (like finding food it can digest), they do not appear to be insurmountable: 🧵

In his book “The Nature of Statistical Learning” V. Vapnik wrote: “When solving a given problem, try to avoid a more general problem as an intermediate step”

See you at #NeurIPS2024, where we are presenting the latest Peptone.io paper @workshopmlsb.bsky.social www.mlsb.io/papers_2024/...

📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at www.plumed-tutorials.org

Now something that is extremely hard to sample with all-atom MD: a big intrinsically disordered protein (IDP) like Complexin II. Different answers depending on MD forcefield. BioEmu - not traind on IDPs - looks reasonable, agrees with experimental evidence and is super fast.

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

Do you want to work at the interface of molecular simulations, structural biology experiments and #AI? Come to Paris for a PhD at @pasteur.fr 1 PhD position is available in our lab funded by ERC_Research. Please repost!! #compchem #compbio Info 👇 research.pasteur.fr/b/15Hr

I am going to read this in detail, congratulation to @franknoe.bsky.social and the team! www.biorxiv.org/content/10.1...

Your talk in Copenhagen reminded me of some work we did where we showed that if you combine a FF and long-range (coevol) contacts you can determine an accurate structure of CsgA (Tian, JACS, 2015), but that if you switch off the FF then you only get the topology right, ...

Something that's come up in a few conversations and I think is underappreciated: the X-ray / cryo-EM structures you download from the PDB are average structures, but not *typical* structures: very few proteins in your sample actually look like that.

New #openreview from our group at disq.us/p/3145xzw! @bussigio.bsky.social and Ivan Gilardoni reviewed a #preprint by @paulrobustelli.bsky.social on the determination of conformational ensembles for intrinsically disordered proteins, combining molecular dynamics simulations and experimental data