iiinova — where your digital self keeps evolving

Reposted by James Fraser

Prism Science @prismscienceorg.bsky.social · 08/09/2026

We need new ways to understand disease & design drugs. Protein motion holds the answer.

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Stephanie Wankowicz @stephanieaw.bsky.social · 01/09/2026

Methods development is usually sequential: Collect, then process, then model, then encode, then interpret. At the @diffuseproject.bsky.social, we tackled all of these pieces once. That is what it takes to transform the field and unlock protein dynamics. See more: diffuse.science/posts/year-o...

diffuse.science

A Year (plus) of DiffUSE

Science progress over the first year-ish of the DiffUSE Project

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Reposted by James Fraser

Stephanie Wankowicz @stephanieaw.bsky.social · 27/08/2026

New pub from @diffuseproject.bsky.social! Ordered water molecules mediate protein stability, ligand binding, and catalysis. Predicting them lags far behind protein structure prediction. We developed WaterFlow, a new state-of-the-art method for ordered water placement. www.biorxiv.org/content/10.6...

biorxiv.org

WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures

Ordered water molecules mediate many protein functions, including stability, ligand binding, and catalysis. Predicting their positions with sub-angstrom accuracy would support protein design, binding ...

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Reposted by James Fraser

Richard Sever @richardsever.bsky.social · 13/07/2026

I recently reviewed a paper for a high-impact journal. It was deeply flawed and rejected based on my review. Hey presto it appears unchanged in a journal I'd never heard of 6 months later... 4/n

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James Fraser @fraserlab.com · 05/07/2026

While there are parts of this manuscript that seem to be overhyped, I don't think peer review alone is the solution you make it out to be here. My bet is that this will appear in a "peer reviewed" venue before too long - and that the content will only be modestly changed. 1/

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Stephanie Wankowicz @stephanieaw.bsky.social · 14/06/2026

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/

podcasts.apple.com

Daylight

Podcast Episode · The Tortured Proteins Department · June 13 · 55m

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Reposted by James Fraser

Giulia Palermo @giuliapalermo.bsky.social · 08/05/2026

Excited to co-organize the @keystonesymposia.bsky.social on Integrative Structural Biology with Alex De Marco @NewYorkStructuralBiology and Niccolò Banterle @embl.org! ⭐️Stellar speakers & keynote by @fraserlab.com! keystonesymposia.org/conferences/... RETWEET&APPLY #KSStructuralBio27 #CryoEM #AI

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Stephanie Wankowicz @stephanieaw.bsky.social · 07/04/2026

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...

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Stephanie Wankowicz @stephanieaw.bsky.social · 06/04/2026

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 .

diffuse.science

The DiffUSE Project

Unlocking Protein Dynamics

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Stephanie Wankowicz @stephanieaw.bsky.social · 12/03/2026

Excited to share Sampleworks led by @karsonchrispens.bsky.social with @diffuseproject.bsky.social. It's a modular framework connecting structure predictors to experimental data and guidance methods. Swap predictors or guidance methods. All open and made to be built upon. t.co/fvNHH3gfVu

t.co

https://diffuse.science/posts/sampleworks/

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Reposted by James Fraser

Stephanie Wankowicz @stephanieaw.bsky.social · 22/02/2026

12th episode (full year!) of the Tortured Protein Department Podcast with@fraserlab.com! podcasts.apple.com/us/podcast/s...

podcasts.apple.com

Science-ing Through the Lightning Strikes

Podcast Episode · The Tortured Proteins Department · February 22 · 1h 5m

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James Fraser @fraserlab.com · 16/02/2026

Do we need a go-fund-me for a Claude Code Max subscription for @jeremymberg.bsky.social to unlock even more valuable reports?

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Reposted by James Fraser

Ben Barad @baradlab.com · 04/02/2026

I've been working on Surface Morphometrics for a new version (coming soon), and made some significant (AI-assisted) performance improvements, especially in pycurv (20-50x!). If you've had technical issues or just felt like it was too slow, give it another try! #teamtomo github.com/GrotjahnLab/...

github.com

GitHub - GrotjahnLab/surface_morphometrics: Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging.

Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging. - GrotjahnLab/surface_morphometrics

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Margot Finn @eicathomefinn.bsky.social · 03/02/2026

'to treat peer review as a throughput problem is to misunderstand what is at stake. Review is not simply a production stage in the research pipeline; it is one of the few remaining spaces where the scientific community talks to itself.' 1/3

timeshighereducation.com

AI is not a peer, so it can’t do peer review

If we still believe that science is a vocation grounded in argument, curiosity and care, we can’t delegate judgement to machines, says Akhil Bhardwaj

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Reposted by James Fraser

Stephanie Wankowicz @stephanieaw.bsky.social · 27/01/2026

New TTPD with @fraserlab.com! We chat about travels, new preprints, and vibe coding. podcasts.apple.com/us/podcast/b... open.spotify.com/episode/6QCR...

podcasts.apple.com

Back to December

Podcast Episode · The Tortured Proteins Department · 01/27/2026 · 52m

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Reposted by James Fraser

Stephanie Wankowicz @stephanieaw.bsky.social · 21/01/2026

New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! www.biorxiv.org/content/10.6...

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Reposted by James Fraser

paulschanda.bsky.social @paulschanda.bsky.social · 21/01/2026

A recent podcast by Stephanie Wankowicz and James @fraserlab.com picked up our work (with Alex Bronstein & coworkers) on Guiding AlphaFold3 with experimental data (cryoEM, X-ray, NMR) to generate protein ensembles. (Thanks for the kind words 🙂) 👉 creators.spotify.com/pod/profile/... (from 35:50)

creators.spotify.com

Episode 8: Open Science in a Changing Academic World by The Tortured Proteins Department

Topics:Compact for Academic Excellence in Higher EducationGovernment ShutdownHHMI's new open science policiesShrinking PhD poolsThe Nobel PrizesThe BearTLOS ReactionsPreprint: Experiment-guided AlphaF...

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Reposted by James Fraser

Jason Rasgon @vectorgen.bsky.social · 12/01/2026

As soon as NIH decided that preprints were A-OK we started preprinting everything. The biggest negative is that now once we've preprinted I lose interest in the actual peer-reviewed article. Which for me isn't a big deal (I'm tenured) but my folk aren't. So I need to force myself to keep up on it

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Reposted by James Fraser

Ben Barad @baradlab.com · 08/01/2026

Happy new year #teamtomo! We've resumed our OHSU tomo journal club, and this year I am going to be sharing it on bluesky. This week we did a roundtable, where attendees each brought a paper and did a 3-5 minute discussion of what they thought was cool about it. Here are the papers they discussed!

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James Fraser @fraserlab.com · 07/01/2026

A reverse K99 would be interesting... 2 or 3 years of R01 type funding to wind down followed by 2-3 years of funding for supplies as you are hosted as an emeritus professor - and ineligible for future grants as a PI

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Reposted by James Fraser

Andrew Ecker @eckerchembio.bsky.social · 06/01/2026

What an extraordinary joy it is to finally be able to share this work with the world. If any of you are excited by chemoproteomics or new tools on the covalent warhead toolbox I think this paper may be right up your alley 💕

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Reposted by James Fraser

Richard Sever @richardsever.bsky.social · 03/01/2026

I personally favor the notion "peer-reviewed" just means a paper with peer reviews, as opposed to a paper that's deemed to have passed some (ill) defined bar as a result. But I'm skeptical the community will embrace that - and even if it does I suspect they'll want curation steps with bars. 5/n

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James Fraser @fraserlab.com · 31/12/2025

Nice to see an acknowledgement (and citation!) of our @prereview.bsky.social in the final version of this awesome paper (www.nature.com/articles/s41...) from @pilarcossio.bsky.social @sonyahanson.bsky.social investigating the promise and limitations of conformational heterogeneity analyses in CryoEM

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James Fraser @fraserlab.com · 30/12/2025

And if collecting and analyzing X-ray structures at scale like this are your thing (or if you want to make it your thing), reach out! We are recruiting at the postdoc or staff scientist level Work on fun targets in the drug discovery/anti-target or neuro space!

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James Fraser @fraserlab.com · 29/12/2025

I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests. Thread below - but first some links: A longer take: fraserlab.com/2025/12/29/k... Preprint: www.biorxiv.org/content/10.6...

fraserlab.com

Know when to co-fold'em

This is the official web page for the James Fraser Lab at UCSF.

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Reposted by James Fraser

bioRxiv Biophysics @biorxiv-biophys.bsky.social · 29/12/2025

Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens www.biorxiv.org/content/10.64898/20…

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Reposted by James Fraser

AI x Bio Discovery @aixbiobot.bsky.social · 29/12/2025

Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens [new] Mac1 co-folding eval: Pose prediction, conform. change, & hit ID post-training.

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Reposted by James Fraser

Stephanie Wankowicz @stephanieaw.bsky.social · 20/12/2025

Last TTPD of the year! We talk about trends over 2025 and predictions for 2026 and beyond! @fraserlab.com podcasts.apple.com/us/podcast/s...

podcasts.apple.com

Science Tree Farm

Podcast Episode · The Tortured Proteins Department · 12/20/2025 · 1h 7m

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Stephanie Wankowicz @stephanieaw.bsky.social · 01/12/2025

New preprint! Entropy drives molecular recognition, yet most structure-based drug design ignores it because it is difficult to measure. X-ray crystallography captures ensembles, not single structures. Can we extract thermodynamically meaningful entropy from them? www.biorxiv.org/content/10.1...

biorxiv.org

Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain

Structure-based drug design has traditionally focused on optimizing static, enthalpic interactions between ligands and proteins or on displacing binding site solvent molecules to entropically favor bi...

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Reposted by James Fraser

bioRxiv Biophysics @biorxiv-biophys.bsky.social · 27/11/2025

Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain www.biorxiv.org/content/10.1101/202…

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Stephanie Wankowicz @stephanieaw.bsky.social · 24/11/2025

TTPD Episode 9 with @fraserlab.com: I Can Do It With a Broken Grant Cycle (Sorry for the crappy audio in places!) Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools wankowiczlab.com/2025/11/24/T...

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Reposted by James Fraser

Andy Kilianski @andykilianski.bsky.social · 27/10/2025

Can’t wait to be there repping @arpa-h.bsky.social and spreading the word about amazing work happening with @fraserlab.com, @qbi-ucsf.bsky.social, and others!

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Reposted by James Fraser

Stephanie Wankowicz @stephanieaw.bsky.social · 23/10/2025

TTPD #8 with @fraserlab.com: Open access, Clear science, Full hearts, Can’t lose! We chat about the Compact for Academic Excellence in Higher Education, HHMI open access, the government shutdown, the BEAR, the Nobel Prizes, and The Life of a Showgirl! wankowiczlab.com/2025/10/23/T...

wankowiczlab.com

The Tortured Proteins Department, Episode 8

This is the official web page for the Stephanie Wankowicz Lab at Vanderbilt University.

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Stephanie Wankowicz @stephanieaw.bsky.social · 21/10/2025

Two main ways to encode structural heterogeneity beyond B-factors or TLS: multiconformer or multi-model (ensemble) models.

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Seemay Chou @seemaychou.bsky.social · 21/10/2025

I spend a lot of time talking to potential grantees about our open science policy. Some field notes here: open.substack.com/pub/seemay/p...

open.substack.com

Why careerism can be bad for science training

Some field notes from scholarly publishing discussions with scientists

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Prism Science @prismscienceorg.bsky.social · 07/10/2025

The Diffuse Project is looking for an amazing Project Manager to help us achieve our goal of unlocking protein dynamics! Are you a scientist who naturally loves organization, coordination, problem solving and working with a diverse team of scientists & engineers?

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Prachee Avasthi @pracheeac.bsky.social · 04/10/2025

New Blog Post: Scholarly Communication Is a Research Problem. This Means You. pracheeac.substack.com/p/scholarly-...

pracheeac.substack.com

Scholarly Communication Is a Research Problem. This Means You.

Scholarly Communication Is a Research Problem.

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Tina Perica @glukozica.bsky.social · 28/09/2025

First work on kinases from my lab! Working on this project, I often remembered the late Cyrus Chothia who said that if the data doesn’t fit a beautiful model, maybe it’s not the model, maybe you just need more data. :)

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Stephanie Wankowicz @stephanieaw.bsky.social · 27/09/2025

TTPD #7 with @fraserlab.com. We chatted about the recent meetings, news, preprint engagement notifications, and the point of rotations. wankowiczlab.com/2025/09/27/T... Spotify: open.spotify.com/episode/0JCB...

wankowiczlab.com

The Tortured Proteins Department, Episode 7

This is the official web page for the Stephanie Wankowicz Lab at Vanderbilt University.

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Reposted by James Fraser

Oli Clarke @olibclarke.bsky.social · 26/09/2025

Also want to highlight that Takanori Nakane made some very helpful and constructive comments about our preprint, which we plan to address in a revised version: disq.us/p/33zqohj

disq.us

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Michael Eisen @mbeisen.bsky.social · 25/09/2025

Technically correct, but proper way to say that is that AAAS and Cell Press publishing policies are incompatible with the open research sharing policies of HHMI.

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 25/09/2025

You are of course correct. Will be interesting to see whether the journals, authors or HHMI adapt

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Jase Gehring @skyjase.bsky.social · 22/09/2025

fun way to combine open discussion with formal communication - post your review on social media!

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James Fraser @fraserlab.com · 22/09/2025

My colleague Joe Bondy-Denomy and I wrote a brief comment on the @brianhie.bsky.social @arcinstitute.org preprint on bacteriophage generation: prereview.org/reviews/1717... tldr: would be nice to have baselines of successful assembly+resistance from lightweight models to test importance of genAI!

prereview.org

PREreview of “Generative design of novel bacteriophages with genome language models”

Authored by James Fraser and Joseph Bondy-Denomy

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