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 · last mo.

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 · 6mo 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/

MadScientist@mads100tist.bsky.social · 6mo 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 · 7mo 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 · 7mo 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 · 7mo 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 · 7mo 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

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

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

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!

James Fraser@fraserlab.com · 7mo ago

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...

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...

Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens https://www.biorxiv.org/content/10.64898/2025.12.25.696505v1

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.

You love to see it!

Online today, the journal version of our ( @nanigrotjahn.bsky.social @attychang.bsky.social @mmedina300kv.bsky.social) manuscript from earlier this year describing membrane thickness measurement in cells with #teamtomo! rupress.org/jcb/article/...