iiinova — where your digital self keeps evolving

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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Hannah Wayment-Steele @hkws.bsky.social · 03/06/2026

Last weekend the W-S lab had our first lab retreat. Activities ranged from kayaking to vibe-coding science games! Thanks to Kemp station @uwmadisoncals.bsky.social for having us!

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Hannah Wayment-Steele @hkws.bsky.social · 01/06/2026

In the W-S lab's first preprint, we describe how genomic language models know something about RNA thermodynamics. Though we think this is cool, things get tricky! A growing practice for interpreting LMs is to perturb input tokens, often called "Categorical Jacobian": 👇

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Hannah Wayment-Steele @hkws.bsky.social · 17/05/2026

For any #nmr chemical shift aficionados, today I ported UCBshift(-X) from Teresa Head-Gordon's lab to work in modern Google Colab. Sharing in case its helpful! @nmr900.bsky.social colab.research.google.com/github/HWaym...

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Hannah Wayment-Steele @hkws.bsky.social · 15/09/2025

Cricket and Willow hosted a W-S lab dinner!

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Reposted by Hannah Wayment-Steele

James Fraser @fraserlab.com · 20/05/2025

We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org. A great position for someone who is looking to be a tech for a few years before grad or med school. aprecruit.ucsf.edu/JPF05424

aprecruit.ucsf.edu

Junior/Assistant/Associate/Full Specialist Positions Available

University of California, San Francisco is hiring. Apply now!

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Reposted by Hannah Wayment-Steele

Stephanie Wankowicz @stephanieaw.bsky.social · 31/03/2025

Join us for the 2nd Macromolecular Conformational Ensembles Conference on June 9th/10th at UCSF. The most compelling questions in structural biology cannot be effectively addressed using only a single structure. conformationalensembles.github.io @fraserlab.bsky.social

conformationalensembles.github.io

Conformational Ensemble

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Reposted by Hannah Wayment-Steele

Gina El Nesr @ginaelnesr.bsky.social · 12/05/2025

someone said we need a meme

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Hannah Wayment-Steele @hkws.bsky.social · 05/05/2025

👏 models in nmr structure != thermodynamics 👏 Structures I’ve been part of include the top-X most probable structures. Same as how the top-X-scoring models from a Rosetta run wouldn’t be a thermodynamic ensemble.

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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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Reposted by Hannah Wayment-Steele

Rita Strack @ritastrack.bsky.social · 10/04/2025

Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.

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Reposted by Hannah Wayment-Steele

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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Reposted by Hannah Wayment-Steele

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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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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Hannah Wayment-Steele @hkws.bsky.social · 18/02/2025

Had a blast talking about topics ranging from the 1966 ALPAC report to pLM pitfalls on isoforms with @uwdsi.bsky.social! Thanks to COMBEE for hosting and recording! www.youtube.com/watch?v=Dxug...

youtube.com

ComBEE Monthly Event: AlphaFold: 25-01-28

YouTube video by UW-Madison Data Science Hub

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Reposted by Hannah Wayment-Steele

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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Hannah Wayment-Steele @hkws.bsky.social · 13/01/2025

Incredible moon over Lake Mendota waiting for the bus that iPhone can hardly do justice Unrelated: looking for recs for tech-sensitive gloves that can handle a “feels like” of -15F 😅

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Hannah Wayment-Steele @hkws.bsky.social · 16/12/2024

If you enjoy MLSB please consider filling out! Statistics may help us craft proposal for next year!

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Hannah Wayment-Steele @hkws.bsky.social · 16/12/2024

MLSB in its 5th year was fantastic! Here’s to passionate people from many backgrounds converging to one overcrowded room!

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Reposted by Hannah Wayment-Steele

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 13/12/2024

📣 Save the dates 📅 We are organizing a Benzon Symposium on "Protein structure prediction and design" with what I think is an amazing set of speakers Meeting will take place in Copenhagen 🇩🇰 on Sept. 1–4, 2025, and abstract submission will open in March (benzon-foundation.dk/benzon-sympo...)

Flyer for a Benzon Symposium on Protein structure prediction and design in biology and pharmacology (Sept. 1–4, 2025). Speakers include: Gabriel Rocklin, Birte Höcker, Amy Keating, Tanja Kortemme, Bruno Correia, Sarel Fleishman, Ashutosh Chilkoti, Minkyung Baek, Noelia Ferruz, James Fraser, Alan Moses, Susan Marqusee, Ben Lehner, Mohammed AlQuraishi, Dek Woolfson, Gustav Oberdorfer, Hannah Wayment-Steele, Ora Schueler-Furman, Jenifer Listgarten, Alexander Rives, & Max Bonomi.

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Hannah Wayment-Steele @hkws.bsky.social · 12/12/2024

First W-S lab dinner, selfie, and 0.5x selfie! Grateful so many awesome people around in what’s technically year -1 of the lab!

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Reposted by Hannah Wayment-Steele

bioRxivpreprint @biorxivpreprint.bsky.social · 09/12/2024

Naturally ornate RNA-only complexes revealed by cryo-EM www.biorxiv.org/content/10.1101/202…

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Hannah Wayment-Steele @hkws.bsky.social · 09/12/2024

Re docking: @workshopmlsb.bsky.social has been piloting a leaderboard for the PLINDER benchmark. It would be awesome to get submissions using existing methods, then everyone can see comparisons better 😁 leaderboard & instructions are on mlsb.io

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Hannah Wayment-Steele @hkws.bsky.social · 22/11/2024

This past year, the organizers at @workshopmlsb.bsky.social partnered with PRX Life to create a special collection focused on the topic of "machine learning in structural biology". Was a pleasure to work together trying to create a venue for workshop papers! journals.aps.org/prxlife/abst...

journals.aps.org

Editorial: Machine Learning for Structural Biology

PRX Life 2, 040001 (2024)

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Hannah Wayment-Steele @hkws.bsky.social · 13/11/2024

Hello again Bluesky! Excited to gain another platform that I do a bad job at checking

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Hannah Wayment-Steele @hkws.bsky.social · 29/12/2023

It took me this long to figure out that on a mac, option-m = µ. goodbye forever us, um, uM. Look at me, typing µ's this easy! Look there's another one. µ

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Hannah Wayment-Steele @hkws.bsky.social · 29/10/2023

A nice Sunday morning where one of us is working on job applications and one of us is destroying a cardboard box.

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Hannah Wayment-Steele @hkws.bsky.social · 22/10/2023

Hello world! (aka, Bluesky) Have you had a fun weekend? I sure did!

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