We will be hosting 4th Full Circle Symposium for Native Biologists hosted at UCSF in May 2027! We aim to build community and provide meaningful opportunities for Native scientists. If you are a Native biologist at any training stage who wants to speak, plz fill this out by this 1/31: bit.ly/4kh5GFx

🚨New preprint! Ligands at the same GPCR can produce wildly different signaling outputs. Why? We built a mutational scanning platform to measure ~10,000 µOR variants across 15 opioids, yielding ~400k measurements of how sequence and ligand chemistry set signaling. www.biorxiv.org/content/10.6... 1/10

In response to the government’s renaming of AI to SI, I propose all journals rename Supplemental Information to Additional Information.

I hear so much about the growing power of predictive biology, especially in drug discovery and "co-folding". I want to see people put their GPU budget where their mouth is!

Come be my colleague at UCSF! Our department BTS (like the K-pop band, but aka Bioengineering and Therapeutic Sciences) is searching for TWO new faculty members. Links, timeline, and why two searches in this thread 🧵

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

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...

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...

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 ...

biorxiv.org

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

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/

Buzz Baum@buzzbaum.bsky.social · 4mo ago

In making its case, the text www.biorxiv.org/content/10.6... plays loose with usual notions of: I) A paper (intro (summary of field), results, figures, methods, discussion) II) A cell III) Semipermeable membrane (has holes), growth (via fusion), division (via external force), cell cycle, heredity…

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

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

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

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

Radial is live! A new organization at @asterainstitute.bsky.social bringing together structural biologists, engineers, and ML scientists to redesign how we do science. @statnews.com has the story: www.statnews.com/2026/03/11/r...

New nonprofit launches with at least $500 million to modernize scientific process for AI era

A new nonprofit called Radial is launching with at least $500 million to modernize the scientific process for the AI era.

statnews.com

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

Science-ing Through the Lightning Strikes

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

podcasts.apple.com

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

Jeremy Berg@jeremymberg.bsky.social · 9mo ago

A brief Bluetorial about analyzing federal grant funding. Both NIH and NSF make data available about funded grants, but each has its quirks and the data structures are VERY different. 1/11

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 - 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

github.com

'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

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

timeshighereducation.com

Post your reviews! And only review preprints - helps with this: fraserlab.com/reviews/

MwahahahahahadScientist@mads100tist.bsky.social · 9mo ago

It breaks my heart every time I review a paper that needs a lot of work, it gets rejected, and then I see it out in another journal with no changes whatsoever

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...

Back to December

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

podcasts.apple.com

🤯

Stephanie Wankowicz@stephanieaw.bsky.social · 9mo ago

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...

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...

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)

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

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!

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

Alex Guseman@alexguseman.bsky.social · 10mo ago

My postdoc advisor is an advocate for the “post faculty fellow” positions and in theory it sounds like a super cool idea. That being said if anyone is wanting to do one in my lab, Please email me a CV and cover letter.

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 💕

Balyn Zaro@balynzaro.bsky.social · 10mo ago

Is arginine the new cysteine?! Check out our lab's latest in collaboration with @ianseiple.bsky.social's team where we introduce ninhydrin as a selective covalent warhead and probe targeting reactive arginines. www.biorxiv.org/content/10.6...

Yes. This is a problem! fraserlab.com/2025/09/08/N... @prereview.bsky.social @richardsever.bsky.social

Janani Durairaj (Jay)@ninjani.bsky.social · 10mo ago

Thanks a lot for the review! We somehow missed it until quite recently but I think addressed a good chunk of the comments in revision anyway, looking forward to your thoughts when it's out