ginaelnesr.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

someone said we need a meme

submitted 16 days ago • 1 comment

"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_...

submitted 31 days ago • 5 comments

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 24 days ago • 9 comments

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

submitted 31 days ago • 1 comment

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

submitted 36 days ago • 2 comments

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!

submitted 36 days ago • 0 comments

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...

submitted 41 days ago • 3 comments

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 ❄️ 🔬

submitted 60 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 63 days ago • 4 comments

Very interesting thread on protein structure dynamics

submitted 64 days ago • 0 comments

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

submitted 64 days ago • 0 comments

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...

submitted 64 days ago • 0 comments

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...

submitted 69 days ago • 1 comment

Interesting thread and preprint on learning protein dynamics from NMR datasets

submitted 69 days ago • 0 comments

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

submitted 69 days ago • 2 comments

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! 🧵

submitted 69 days ago • 5 comments

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

submitted 70 days ago • 1 comment

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

submitted 70 days ago • 0 comments

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. 🍝 💊🧲 💻 🦠

submitted 107 days ago • 3 comments

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...

submitted 108 days ago • 1 comment

🧬🧪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

submitted 109 days ago • 3 comments

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

submitted 149 days ago • 3 comments

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

submitted 160 days ago • 8 comments

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... 🧬🧶

submitted 163 days ago • 6 comments

a good benchmark only cost me 22 CAD

submitted 163 days ago • 0 comments

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

submitted 164 days ago • 0 comments

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

submitted 164 days ago • 0 comments