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James Fraser

@fraserlab.com
3.7K followers 513 following 284 posts

Professor and Chair @UCSF/@UCSF_BTS - dynamic structural biology and open science - (he/him) - fraserlab.com

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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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Reposted by James Fraser
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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James Fraser @fraserlab.com · 18/08/2026
Zapier! zapier.com.
zapier.com
Zapier: Automate AI Workflows, Agents, and Apps
Build and scale AI workflows and agents across 9,000+ apps with Zapier—the most connected AI orchestration platform. Trusted by 3 million+ businesses.
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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
There are challenges for sure - but let's also not pretend that the journal gatekeeping system prevents abuse or gives absolute signals-of-trust 3/
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James Fraser @fraserlab.com · 05/07/2026
Lots of papers with hype pass peer review (Arsenic Life springs to mind) What's cool here is that there is now a preprint! Comment away - not just on here. Write a @prereview.bsky.social or use the new "hypothesis" layer to comment on @biorxivpreprint.bsky.social : openrxiv.org/hypothesis-c... 2/
openrxiv.org
Introducing Hypothesis commenting on bioRxiv and medRxiv: an updated way to engage with preprints - openRxiv
An important part of our mission at openRxiv is to collaborate with other organizations to improve science communication and promote interoperability. Preprints are just one part of the research workf...
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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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James Fraser @fraserlab.com · 17/04/2026
Sad to miss this year- overlaps with ucsf graduation!
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Reposted by James Fraser
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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Reposted by James Fraser
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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James Fraser @fraserlab.com · 07/04/2026
🙏 author email notifications. This will lead us back to posting directly on site! we had stopped using disqus in favor of @prereview.bsky.social
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James Fraser @fraserlab.com · 26/03/2026
I almost guessed it based on the two arms with what I presume are unusual detectors - should have been more bold!!!
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James Fraser @fraserlab.com · 26/03/2026
ESS!!! Basically part of the larger maxiv ecosystem.
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James Fraser @fraserlab.com · 26/03/2026
Oak ridge?
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James Fraser @fraserlab.com · 26/03/2026
💎
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James Fraser @fraserlab.com · 26/03/2026
Max iv?
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James Fraser @fraserlab.com · 14/03/2026
Code?
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Reposted by James Fraser
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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James Fraser @fraserlab.com · 11/03/2026
great preprint Alex!!!
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James Fraser @fraserlab.com · 11/03/2026
I agree - we have been trying to assess how different models do in a challenging DMS test case (+/- different inhibitors - pmc.ncbi.nlm.nih.gov/articles/PMC...) - we use a very stringent test set that held out positions and residues, finding that most models do not perform well...
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Reposted by James Fraser
Prism Science @prismscienceorg.bsky.social · 11/03/2026
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...
statnews.com
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.
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James Fraser @fraserlab.com · 07/03/2026
Congrats!!!
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James Fraser @fraserlab.com · 28/02/2026
Great read, one small correction - pretty sure it's Dan's wife Marian who was nicknamed "Bunny" not Dan Koshland...
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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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Reposted by James Fraser
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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James Fraser @fraserlab.com · 01/02/2026
On the plus side - hallucination is dramatically lower now than a year ago. In the downside- peer review should be fun an a mental exercise (two things you should never outsource to AI)
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James Fraser @fraserlab.com · 01/02/2026
Post your reviews! And only review preprints - helps with this: fraserlab.com/reviews/
fraserlab.com
Peer Reviews from the Fraser Lab
This is the official web page for the James Fraser Lab at UCSF.
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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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James Fraser @fraserlab.com · 21/01/2026
🤯
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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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James Fraser @fraserlab.com · 12/01/2026
Do you have a repo I can look at invite github.com/fraserlab if private if you are comfortable?
github.com
fraserlab - Overview
fraserlab has 2 repositories available. Follow their code on GitHub.
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James Fraser @fraserlab.com · 12/01/2026
This is cool - is it: app.benchmate.ai/pricing or something you are writing?
app.benchmate.ai
Benchmate.ai
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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
Me too. Just trying to brainstorm ideas that might incentivize more retirement without a forcing function of a hard cutoff
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James Fraser @fraserlab.com · 07/01/2026
Sorry. I misread! Many reacting strongly the other way - they should just be forced to retire at age X.
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James Fraser @fraserlab.com · 07/01/2026
I think the trouble is that people are still competitive- and don’t have an off-ramp for their identity as a scientist. I’m with you, I’ll exit stage right when the time comes. But I see many who don’t….
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James Fraser @fraserlab.com · 07/01/2026
from: hhmicdn.blob.core.windows.net/policies/Inv... "expanded phase out" of 5 years, rather than going through competitive renewal (7 years if successful and 2 years if not)
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James Fraser @fraserlab.com · 07/01/2026
Based partially on observations of this working: bsky.app/profile/fras...
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James Fraser @fraserlab.com · 07/01/2026
A point in favour of this: an off ramp exists for HHMI investigators and many actually take it
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James Fraser @fraserlab.com · 07/01/2026
I agree it’s hard. Much like convincing them to retire. But the alternative isn’t retiring. It’s renewing their R01.
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James Fraser @fraserlab.com · 07/01/2026
People just don’t do it though. I think an off-ramp program would allow people to hold their heads high, maintain identity as a scientist ,etc. Trying to brainstorm policy ways to get people to do actually do it.
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James Fraser @fraserlab.com · 07/01/2026
Great. I don’t think advocating for either or both of these are mutually exclusive. Need many policy ideas for this problem…
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James Fraser @fraserlab.com · 07/01/2026
Tenure is tenure. www.nytimes.com/1990/10/21/s... And I knew and really loved Howard (TAed his ethics class for many years)…
nytimes.com
Campus Life: Berkeley; Biochemist, 71, Fights Mandatory Retirement (Published 1990)
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