12th episode (full year!) of the Tortured Protein Department Podcast [email protected]! podcasts.apple.com/us/podcast/s...

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

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/...

'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

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

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...

🤯

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

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 💕

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

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!

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/...

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...

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...

Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain https://www.biorxiv.org/content/10.1101/2025.11.25.690589v1

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...

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!

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...

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

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...

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?

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

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. :)

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...

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

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.

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

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

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!

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

The last day for public comment on this topic is Monday, Sept 15. It’s time to unleash science. 3/3 Gift link to op-ed: www.wsj.com/opinion/acad... NIH Request for Information: grants.nih.gov/grants/guide...

Right now is the best chance the scientific community has ever had to end the artificial scarcity of academic journals. 1/

If the authors are aware the review occurred!

Community Reviews are science in real time! Check out this new and recent example of open feedback in action: Hale et al.’s preprint got reviewed by a community-organized group through PREreview and then the authors replied to it. 📄 doi.org/10.1101/2025... #OpenScience #Preprints #CommunityReview

This! Many people have expert opinions about their specific interest in a paper just from reading it that would be helpful. It needn’t be comprehensive to be exceptionally helpful, especially since people’s expertise can rarely cover the joint expertise of increasingly collaborative work anyway

I love writing spontaneous and unsolicited reviews. I would be thrilled folks did it to me too! I think it gets the heart of what we do science for - giving and getting feedback to get closer to the ‘truth’! Otherwise why post a preprint if you don’t want people to read and respond?

Great point. Make it opt out, not opt in, for authors to see feedback. We need to grow a culture of rapid and constructive feedback to replace ‘peer review’… which is outdated, was not designed and is not fit for purpose. How can we do that if public reviews are not even seen by the authors?

I was discouraged from giving biorxiv reviews when I realized they are buried as soon as a new version is posted.

Absolutely has happened to me. bsky.app/profile/esch...

This has happened to me as well bsky.app/profile/esch...