iiinova — where your digital self keeps evolving

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Hannah Wayment-Steele @hkws.bsky.social · 21/08/2026

@ginaelnesr.bsky.social and I are excited to release makeshift -- a lightweight package to lower the barrier for using NMR dynamics data in ML. We hope this can pave the way for more NMR-based models like Dyna-1! Preprint: biorxiv.org/content/10.6... Docs: makeshift-docs.readthedocs.io

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Reposted by Gina El Nesr

bioRxiv Biophysics @biorxiv-biophys.bsky.social · 20/08/2026

Makeshift: a lightweight software for accessing and analyzing NMR data and protein dynamics www.biorxiv.org/content/10.64898/20…

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BejaLabTechnion @bejalab.bsky.social · 11/08/2026

Learning millisecond protein dynamics from what is missing in NMR spectra www.nature.com/articles/s41...

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bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 25/04/2026

Zero-shot design of a de novo metalloenzyme www.biorxiv.org/content/10.64898/20…

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Gina El Nesr @ginaelnesr.bsky.social · 28/04/2026

Excited to report the first zero-shot designed, de novo enzyme catalyzing two of the most energetically demanding reactions in biology—phosphomonoester and phosphodiester hydrolysis—with catalytic efficiencies comparable to natural enzymes! 🚀 /🧵 @stanfordbiosci.bsky.social @simonduerr.eu

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 20/01/2026

Another day, another paper describing an ML method for generating conformational ensembles without comparison to any experimental data 😩

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Milot Mirdita @milot.bsky.social · 20/01/2026

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

mirdita.org

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning

Mirdita Lab builds scalable bioinformatics methods.

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Boston Protein Design and Modeling Club @bpdmc.org · 22/11/2025

Don't fret if you weren't in the room this week when @ginaelnesr.bsky.social gave her stellar seminar because you can check out the recording 👇 youtu.be/I-utRMS84E8

youtu.be

Learning millisecond protein dynamics from what is missing in NMR spectra

YouTube video by Boston Protein Design and Modeling Club

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Gabriel Rocklin @grocklin.bsky.social · 19/11/2025

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

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Boston Protein Design and Modeling Club @bpdmc.org · 12/11/2025

We can't wait until Wednesday, November 19th 2025 to arrive because we have @ginaelnesr.bsky.social from @possuhuanglab.bsky.social speaking at 7pm EST in Room 6055, Longwood Center, @danafarber.bsky.social "Learning millisecond protein dynamics from what is missing in NMR spectra" bpdmc.org

bpdmc.org

schedule

introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...

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Gina El Nesr @ginaelnesr.bsky.social · 12/09/2025

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

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Diego del Alamo @delalamo.xyz · 21/08/2025

... 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

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Will Ratcliff @wcratcliff.bsky.social · 12/08/2025

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.

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Martin Pacesa @martinpacesa.bsky.social · 25/07/2025

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!

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Gina El Nesr @ginaelnesr.bsky.social · 28/07/2025

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!🌟

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Gina El Nesr @ginaelnesr.bsky.social · 08/07/2025

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

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The Align Foundation @alignbio.bsky.social · 08/07/2025

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

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Noelia Ferruz @noeliaferruz.bsky.social · 07/07/2025

Noooo😭 This was the BEST workshop at NeurIPS!!

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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 07/07/2025

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

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Gina El Nesr @ginaelnesr.bsky.social · 07/07/2025

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…

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Alexey Amunts @amunts.bsky.social · 04/07/2025

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.

science.org

Exclusive: Famed protein structure competition nears end as NIH grant money runs out

Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold

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Science Magazine @science.org · 02/07/2025

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

scim.ag

Exclusive: Famed protein structure competition nears end as NIH grant money runs out

Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 02/07/2025

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...

doi.org

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant | PNAS

The correlation between synonymous codon usage and secondary structure in translated proteins has been widely demonstrated. This usage plays a capi...

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Gina El Nesr @ginaelnesr.bsky.social · 23/06/2025

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

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Diego del Alamo @delalamo.xyz · 27/04/2025

"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_...

delalamo.xyz

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 04/05/2025

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.

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Hannah Wayment-Steele @hkws.bsky.social · 28/04/2025

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.

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Hannah Wayment-Steele @hkws.bsky.social · 28/04/2025

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*

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Gina El Nesr @ginaelnesr.bsky.social · 22/04/2025

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

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Diego del Alamo @delalamo.xyz · 21/04/2025

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

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/04/2025

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...

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 29/03/2025

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 ❄️ 🔬

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Gabriel Rocklin @grocklin.bsky.social · 26/03/2025

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!

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Andrew Roger @andrewjroger.bsky.social · 25/03/2025

Very interesting thread on protein structure dynamics

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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 25/03/2025

Large-scale discovery, analysis, and design of protein energy landscapes www.biorxiv.org/content/10.1101/202…

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Gina El Nesr @ginaelnesr.bsky.social · 25/03/2025

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...

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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 20/03/2025

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...

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Simon Bayly @simonbayly.bsky.social · 20/03/2025

Interesting thread and preprint on learning protein dynamics from NMR datasets

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Hannah Wayment-Steele @hkws.bsky.social · 20/03/2025

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

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Gina El Nesr @ginaelnesr.bsky.social · 20/03/2025

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! 🧵

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 19/03/2025

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

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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 19/03/2025

Learning millisecond protein dynamics from what is missing in NMR spectra www.biorxiv.org/content/10.1101/202…

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Gabi Heller @g-heller.bsky.social · 11/02/2025

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. 🍝 💊🧲 💻 🦠

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