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Hannah Wayment-Steele

@hkws.bsky.social

Avid rower who sometimes thinks about biomolecular dynamics. Asst Prof @uwbiochem.bsky.social https://waymentsteelelab.org/

63 Posts1144 Follower105 Folgt
Hannah Wayment-Steele@hkws.bsky.social · 2mo ago

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 · last yr.

The W-S lab is seeking to hire a research scientist! This person will lead wet-lab innovations in our team as we combine AI and experiments to understand and design dynamics! Thanks for sharing/RTs! jobs.wisc.edu/jobs/scienti...

Scientist and Lab Operations Coordinator - Madison, Wisconsin, United States

Job Summary: The Wayment-Steele Lab seeks a Research Scientist to lead experimental operations within our highly interdisciplinary team, integrating both computational "dry" and experimental "wet" l...

jobs.wisc.edu

Hannah Wayment-Steele@hkws.bsky.social · last yr.

👏 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.

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · last yr.

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.

Hannah Wayment-Steele@hkws.bsky.social · last yr.

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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Diego del Alamo@delalamo.xyz · last yr.

"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_...

ML for Protein Engineering Seminar@ml4proteins.bsky.social · last yr.

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!

Learning millisecond protein dynamics from what is missing in NMR spectra

Many proteins’ biological functions rely on interconversions between multiple conformations occurring at micro-to millisecond (µs-ms) timescales. A lack of standardized, large-scale experimental data ...

biorxiv.org

Rita Strack@ritastrack.bsky.social · last yr.

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.

Gina El Nesr@ginaelnesr.bsky.social · last yr.

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 · 2y ago

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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