MLSB is coming to Copenhagen, DK 🎉 Submission is under the same portal, just simply indicate your location preference(s).

... each independent simulation is 500 ns long, almost certainly too short to sample the sorts of large-scale functionally relevant conformational changes that ML methods should be learning from, which means I must once again repost this excerpt from Janson et al

Not sure how many scientists here have tried Claude Code or similar command line coding assistants. I had a complicated family property tax problem that was best solved by a brute force Monte Carlo simulation approach, so I spent a few days coding up and analyzing a model with Claude Code.

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬 Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟

molecular cat-formations

Enzyme design! Benchmark data! Wet-lab validation! Expression & activity assays!! ✨

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

Noooo😭 This was the BEST workshop at NeurIPS!!

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year. Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology” More on the future of MLSB soon…

Speak up to prevent a major loss for the field. CASP, which helped shaping structural biology including AlphaFold is on the verge of shutting down. NIH funding has lapsed, UC Davis support ends and the core team is being let go. Painfully shortsighted.

Exclusive: An international scientific competition widely credited with spurring the development of artificial intelligence for biology appears to be on its deathbed. scim.ag/44ukS90

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant doi.org/10.1073/pnas... [Following: Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon doi.org/10.1038/s414...

Ran some sequence design with LigandMPNN and it... designed a protein with an (almost) His-tag 🤔

someone said we need a meme

"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_...

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.

If we wanna make accurate boltzmann samplers, we gotta know what distributions they should be sampling 😁 These change in the presence/absence of ligands, and there are multiple systems for which this is well-understood by this point experimentally.

Really nice resource from @delalamo.xyz !! Wanna mention the "AdK test" we're noticing newer DL methods fall short on: many proteins (like AdK) that have apo/holo conf change sample both the apo/holo state even without ligand bound. But w/o ligand bound, they *are mainly in the apo state*

Super excited to be presenting Dyna-1 next week with @hkws.bsky.social !!

Next Tues (4/29) at **4:30PM** ET, we will have @ginaelnesr.bsky.social @hkws.bsky.social present "Learning millisecond protein dynamics from what is missing in NMR spectra" Paper: biorxiv.org/content/10.1... Sign up on our website for zoom links!

Any NN trained on publicly available MD data needs this disclaimer: trajs that are 100s of ns long are heavily influenced by the starting state and are unlikely to teach the kinds of trends in equilibrium dynamics that scientists are interested in predicting

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...

If you care about how to use cryoEM to estimate conformational ensembles and populations of different states you should read this from @pilarcossio.bsky.social and team ❄️ 🔬

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!

Very interesting thread on protein structure dynamics

Large-scale discovery, analysis, and design of protein energy landscapes https://www.biorxiv.org/content/10.1101/2025.03.20.644235v1

We collaborated with @hf.co 🤗 to host all of our models and data online! Big thank you to @danielvanstrien.bsky.social @wauplin.hf.co @lhoestq.hf.co for helping out (and the GPU)! Dyna-1 and RelaxDB on HF: 🚀 huggingface.co/spaces/gelne... 🌟 huggingface.co/datasets/gel...

Unassigned nitrogens in nmr data often indicate biologically relevant motion in proteins, and this can be used train deep learning models of protein dynamics! Hannah Wayment-Steele @ginaelnesr.bsky.social @sokrypton.org www.biorxiv.org/content/10.1...

Interesting thread and preprint on learning protein dynamics from NMR datasets

Protein dynamics was the first research to enchant me >10yrs ago, but I left in PhD bc I couldn't find big experimental data to evaluate models. Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1. 📝: rb.gy/de5axp

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

Learning millisecond protein dynamics from what is missing in NMR spectra https://www.biorxiv.org/content/10.1101/2025.03.19.642801v1

Today @gogs-k.bsky.social, @tlhr.bsky.social, and I are launching @bindresearch.org, a UK-based not-for-profit research startup to deliver publicly–available tools and datasets to make intrinsically disordered proteins druggable. 🍝 💊🧲 💻 🦠

Excited to share our new AllMetal3D model building on Metal3D. AllMetal3D predicts the location, identity and geometry of the major biologically relevant metal ions doi.org/10.1101/2025...

🧬🧪Protein codes promote selective subcellular compartmentalization | Science www.science.org/doi/10.1126/... Henry Kilgore @itamarchinn.bsky.social @pgmikhael.bsky.social Ilan Mitnikov, et al. @aihealthmit.bsky.social @whiteheadinstitute.bsky.social @mitofficial.bsky.social

Bluetorial: Metal regulation, an unexpected connection, and a deep evolutionary insight

Hi Bluesky, just in time for the holidays I am excited to share the latest pre-print from my group! We solved the 3D structure of a mysterious viral RNA that resists degradation by host nucleases. A short 🧵 &link below – please also check out the full video! #RNA #RNAbiology #RNASky #lovevirology

A periodic reminder that biologically meaningful conformational changes do not have to be large While textbooks may indicate that relevant motions are large, even the original paper on alternating access makes it clear that atoms just need to move a bit to have an effect. doi.org/10.1038/2119... 🧬🧶

Upon further experimentation, this approach is mostly garbage for larger proteins

a good benchmark only cost me 22 CAD

thank you to everyone who came to @workshopmlsb.bsky.social!!! more so, thank you Erika Alden DeBenedictis for the fire crowd-sourced brainstorming 🔥🔥🔥

First off: a great primer and motivation for the workshop by @ginaelnesr.bsky.social !! Amazing to recognize all the researchers (both computational and even experimentalists) that have made the nobel-winning work of AF2 possible!

MLSB happening today! Packed room at @neuripsconf.bsky.social East Building Rm 11-12 @workshopmlsb.bsky.social

We discovered 3 RNA families that form homo-oligomeric RNA-only complexes! Studying nature continues to expand my wildest imagination. Read about it: doi.org/10.1101/2024... Vivian Wu, Svetlana Shabalina, Hyunbin Lee, Grace Nye, Eugene Koonin, Alex Gao, Rhiju Das, Wah Chiu