Stephanie Wankowicz
@stephanieaw.bsky.social
Computational Structural Biologist Scientific Program Director, diffUSE Project (she/her) diffuse.science Past: Vanderbilt, UCSF, Dana-Farber, Broad Institute, UMass Amherst
Most PDB structures report one set of coordinates. But the experimental data behind them, in both X-ray crystallography and cryo-EM, is produced by an ensemble of structures. How to extract this ensemble data at scale has been a quest in structural biology for 40+ years.
Given the clear parallels between the new Vanderbilt "First Principles" and the text of the letter, I would be shocked if Vanderbilt didn't play a large role in the discussions www.vanderbilt.edu/declaration/ Reminder that faculty played no role in drafting or approving the first principles
Declaration
The University and Its Purpose: A Declaration of First Principles was adopted by the Vanderbilt University Board of Trust in June 2026. The declaration is organized around three core purposes: Pathbre...
vanderbilt.edu
Dominique Baker@bakerdphd.bsky.social · 4d agoA) If everyone loved this letter, I feel like we might hear something different from the interview subjects in this article B) I don't think I will be invited to the AAU holiday party www.chronicle.com/article/coll...
⚡ Time is running out! ⚡ The deadline for the @biophysicalsoc.bsky.social Theory & Computation Awards is Sept 15! 🧬💻 Recognizing outstanding research across: 🎓 Postdocs 🌱 Early Career 🚀 Mid-Career Nominate a student or colleague! 🧪✨ 👇 Details: www.biophysics.org/Awards-Fundi...
Subgroup Awards - The Biophysical Society
biophysics.org
In our latest blog, @fraserlab.com graduate student Taylor Womack discusses his roadmap before the results: how he plans to separate lattice vibrations from internal protein motion, which open tools he is using, and which parts are still unresolved. Feedback welcome. diffuse.science/posts/taylor...
Is it all just the lattice?
Towards a complete forward model of diffuse scattering
xtraj.py
“If universities oppose the actions of the administration, they need to say so quickly so that their constituents aren’t left wondering whether there’s a plan. The alternative is a community of university scientists adrift and grasping for a lifeline.” www.science.org/doi/10.1126/...
University science in the US needs a coherent plan
The Trump administration continues to degrade America’s scientific establishment, causing widespread harm to the country’s broader interests and well-being. Last week, the Association of American Univ...
science.org
TTPD Episode 16: Cruel Kinase Summer with @fraserlab.com! We chat about a revolving door of consortium meetings, follow up on the OMB-proposed rule, two mini-protein kinase preprints, and how to share science, including differences between blogs and scholarly work. diffuse.science/posts/TTPD-16/
Cruel Kinase Summer, Episode 16
The Tortured Proteins Department Podcast, Cruel Kinase Summer
diffuse.science
Unlocking protein dynamics requires infrastructure we all can access. ICYMI: all of our software packages live on GitHub, updated in the open: github.com/diff-use
diffUSE
diffUSE has 15 repositories available. Follow their code on GitHub.
github.com
What's happening in protein dynamics research right now? Jaime & Stephanie break down NIH policy changes, preprints & the conformational ensembles conference. New episode up: diffuse.science/posts/TTPD-15/ #StructuralBiology
Modeling the solvent in X-ray structures is HARD, and a key reason for the mismatch between models & experimental data. But being able to test different ways to model bulk solvent and measure its impact on refinement will get us a step closer to figuring out how to account for it.
The DiffUSE Project@diffuseproject.bsky.social · 2mo agoBulk solvent fills ~half a protein crystal. Modeling this is required for a good fit to experimental data. How best to model this remains an open question. New from diffUSE: a Phenix patch to supply your own solvent map (MD, 3D-RISM, EDEN, neural nets). Read more here: thestacks.org/publications...
Excited to present sampleworks: a modular platform for generating biomolecular conformational ensembles by coupling AI structure predictors to experimental data. Our first publication of @diffuseproject.bsky.social, led by @karsonchrispens.bsky.social + Marcus Collins. thestacks.org/publications...
sampleworks: A Modular Platform for Experimentally Guided Biomolecular Ensemble Generation
thestacks.org
TTPD Episode 15 with @fraserlab.com! We chat about our conformational ensembles conference (paired talk FTW!), 4 different preprints, and new NIH disasters. podcasts.apple.com/us/podcast/d... diffuse.science/posts/TTPD-15/
Daylight
Podcast Episode · The Tortured Proteins Department · June 13 · 55m
podcasts.apple.com
A Perspective discusses challenges in macromolecular ensemble prediction and the methodological advances that are needed. @stephanieaw.bsky.social www.nature.com/articles/s41...
From possibility to precision in macromolecular ensemble prediction - Nature Methods
This Perspective discusses current challenges in macromolecular ensemble prediction and the infrastructure and methodological advances needed to overcome these barriers.
nature.com
We present sampleworks, an open, modular platform for generating and evaluating biomolecular conformational ensembles from structure predictors guided by experimental data doi.org/10.82153/jkx....
Closing this chapter means leaving an amazing team. These people took a chance, worked hard, and made the lab a fantastic place to work everyday.
Want to shape the future of structural biology? We are seeking a Project Manager to help lead the DiffUSE Project, guiding ML researchers, computational scientists, national labs, and university partners. Apply: buff.ly/gZlj9AP #StructuralBiology #MachineLearning #Hiring #AcademicSky
Project Manager - DiffUSE Project
ABOUT DIFFUSE The DiffUSE Project is building open infrastructure to study protein dynamics using experimental data. The project spans wet-lab collaborators, computational scientists, ML researchers,…
jobs.ashbyhq.com
Since World War II, the United States built the world’s preeminent scientific enterprise on a straightforward principle: federal dollars should fund the best science, as determined by independent experts rather than politicians. This proposed rule dismantles all of this.
elizabethginexi.bsky.social@elizabethginexi.bsky.social · 2mo agoSummary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...
The DiffUSE Project wants examples where structural heterogeneity matters but cannot be encoded in PDBx/mmCIF. X-ray, cryo-EM, time-resolved, multi-map, or fragment screening data welcome. Submit yours: diffuse.science/submit/
Submit Examples of Heterogeneous Structural Data
The DiffUSE Project
diffuse.science
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...
ICYMI: The latest Tortured Proteins Department episode. @stephanieaw.bsky.social and @fraserlab.com on: NIH strategic plan comments (due 5/26), AI lab guidelines, two new cryo-EM preprints, training scientists for what's next diffuse.science/posts/TTPD-14/
So the Republican Supermajority breaks the law and violates the constitution to strip Memphis of representation — then Speaker Sexton strips Dems of committee assignments for daring to protest. Welcome to Tennessee.
The United States is a constitutional federal representative democracy. Or is it?
Ari Berman@ariberman.bsky.social · 3mo agoBreaking: Tennessee Republicans pass new 9-0 gerrymander after SCOTUS destruction of Voting Rights Act eliminating state’s only majority-Black district & last Democratic seat. Splits Memphis, which is 63% Black, into 3 districts to disenfranchise Black voters. Quite literally a return to Jim Crow
The CASP experiment is about to start - and is still short on challenging prediction targets. Ligand complexes, RNA, …
Torsten Schwede@torstenschwede.bsky.social · 5mo agoIs #AI hitting a plateau in structure prediction? Help us find out at CASP17! 🧪🧬 Calling for Targets: Immune Complexes, protein - ligand complexes, RNA/DNA, conformational ensembles, membrane proteins, viral origins, and large complexes. The Rule of Thumb: If AF3 can’t model it, we want it.
Very good (if tragic) story from the Washington Post [GIft Link] wapo.st/3OONwh6 1/8
For U.S. medical researchers, shrinking labs and bare budgets are the new reality
The Trump administration has slashed the number of grants from the National Institutes of Health, with far fewer focused on women, cancer and mental health.
wapo.st
Excited to announce this postdoc position at the intersection of experiment and computation for time-resolved cryo-EM! It's a collaboration between the Enchev group at the Crick and myself and @pilarcossio.bsky.social at the Flatiron Institute! Plz share. crick.wd3.myworkdayjobs.com/External/job...
Senior Data Scientist
Salary for this Role: From £53,025 per annum plus benefits, subject to skills and experience Job Title: Senior Data Scientist Reports to: Radoslav Enchev Closing Date: 06/May/2026 23.59 GMT Job Descri...
crick.wd3.myworkdayjobs.com
Year 3 of Conformational Ensembles Conference! The most compelling questions in structural biology cannot be effectively addressed with a single structure. We have a stellar lineup of people looking at and answering these questions. @fraserlab.com More information: conformationalensembles.github.io
Conformational Ensemble
conformationalensembles.github.io
Episode 13 Tortured Protein Department Podcast: Long Live with @fraserlab.com! Catch my big news with the @diffuseproject.bsky.social, psycho travel stories, April Fools pranks, and AI grad students. podcasts.apple.com/us/podcast/l...
I'm ecstatic to share that I'm joining the @diffuseproject.bsky.social (diffuse.science) full-time as Scientific Program Director at @asterainstitute.bsky.social .
The DiffUSE Project
Unlocking Protein Dynamics
diffuse.science
ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15
AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network
Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...
rdcu.be
