James Fraser

James Fraser

@fraserlab.com

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

3.7K followers513 following302 posts

James Fraser reposted

Matt Howard
@matthewkhoward.bsky.social

🚨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

James Fraser
@fraserlab.com

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

James Fraser
@fraserlab.com

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!

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James Fraser
@fraserlab.com

If you want a head start, go look at what worked in our PXR challenge for structure prediction (do a lot of AI prediction, score with some physics is one strategy!)

James Fraser
@fraserlab.com

Given a ligand SMILES and nothing else, predict the 3D structure of the CYP3A4 complex. DO IT!!! CYP CYP Hooray!

James Fraser
@fraserlab.com

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!

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James Fraser
@fraserlab.com

I wanted to highlight the structure prediction track because it features 20 novel CryoEM structures of CYP3A4 bound to ligands, collected by Anna Karen Orta!

James Fraser
@fraserlab.com

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!

James Fraser
@fraserlab.com

CYP3A4 metabolizes something like half of the drugs on the market and it is the biggest single source of drug-drug interactions. It would be huge to be able to predict which molecules inhibit CYP3A4 and to modify them to remove this liability!

James Fraser
@fraserlab.com

So if you think you can do structure prediction (or improve structure prediction with MD, etc), you should look at the CYP challenge that we at @openadmet.bsky.social are running right now: huggingface.co/spaces/opena...

huggingface.coOpenADMET CYP Blind Challenge - a Hugging Face Space by openadmetThis Gradio app lets you join the OpenADMET CYP Inhibition Blind Challenge. Upload a CSV or Parquet file with your regression or classification predictions, or a ZIP archive of PDB structures for t...
James Fraser
@fraserlab.com

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 🧵

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James Fraser
@fraserlab.com

Great colleagues including Shuvo Roy, Tony Capra, Tanja Kortemme, Nevan Krogan, Rada Savic, Ryan Hernandez, Nadav Ahituv, Diego Calderon, Sophie Dumont, Kathy Giacomini, Su Guo, Andrej Sali, Seth Shipman, Catera Wilder, Liang Zhao, and others! (Plus honorary members J-Hope, RM, Jung Kook, etc)

James Fraser
@fraserlab.com

Whoops - one more thing: A big advantage of the Bay Area ecosystem is the proximity to both Biotech and AI talent and collaborations. UCSF is a great environment to make sure your scientific interests transcend the traditional boundaries separating academia and industry!

James Fraser
@fraserlab.com

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 🧵

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James Fraser
@fraserlab.com

Timeline: Applications due Oct 30 Chairs and I create a shortlist by Nov 11 Committee reviews Nov 11-30 Zoom interviews before the end of 2026 Committee decides on finalists the first week of January Symposia in March

James Fraser
@fraserlab.com

Is BTS awesome? Yes! We are an exceptionally broad department scientifically, characterized by our quantitative nature and our interest in making discoveries at all scales (atoms to populations).

James Fraser
@fraserlab.com

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 🧵

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James Fraser
@fraserlab.com

Should candidates apply to both? Ideally not. We can send candidates from one search to the other, and they have different focuses. I will be reading EVERY application to make the shortlists with the chairs (Tony and Shuvo). Both committees will see all the talks and chalk talks of all candidates.

James Fraser
@fraserlab.com

Anything unusual about the search? Yes! We will bring candidates from the two searches onsite over 2 visits total. Each visit will be mixed between the two searches, and committee members have blocked off time to attend symposium-style talks on the first day.

James Fraser
@fraserlab.com

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 🧵

View full thread
James Fraser
@fraserlab.com

The biomolecular engineering position is funded through an endowed position guaranteeing salary support similar to a standard UCSF ladder rank faculty appointment (and has the same tenure process, etc).

James Fraser
@fraserlab.com

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 🧵

James Fraser reposted

Stephanie Wankowicz
@stephanieaw.bsky.social

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.orgWaterFlow: Prediction of Ordered Water Molecule Positions on Protein StructuresOrdered water molecules mediate many protein functions, including stability, ligand binding, and catalysis. Predicting their positions with sub-angstrom accuracy would support protein design, binding ...

James Fraser reposted

Richard Sever
@richardsever.bsky.social

Replying to @richardsever.bsky.social

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

James Fraser
@fraserlab.com

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

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…

biorxiv.orgbiorxiv.org
James Fraser
@fraserlab.com

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/

Alex Crits-Christoph@acritschristoph.bsky.social

It is a pretty clear example of the challenges of science without journals [or imaginable future superior signals of in-field trust] In such a world science often becomes a game of who you know, and who has the best media connections and team, and all the (worse, IMO) biases that go with that

James Fraser reposted

Prism Science
@prismscienceorg.bsky.social

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.comNew nonprofit launches with at least $500 million to modernize scientific process for AI eraA new nonprofit called Radial is launching with at least $500 million to modernize the scientific process for the AI era.
James Fraser
@fraserlab.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

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

James Fraser reposted

Ben Barad
@baradlab.com

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.comGitHub - 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

James Fraser reposted

Margot Finn
@eicathomefinn.bsky.social

'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.comAI is not a peer, so it can’t do peer reviewIf we still believe that science is a vocation grounded in argument, curiosity and care, we can’t delegate judgement to machines, says Akhil Bhardwaj
James Fraser
@fraserlab.com

🤯

Stephanie Wankowicz@stephanieaw.bsky.social

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...

James Fraser reposted

paulschanda.bsky.social
@paulschanda.bsky.social

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.comEpisode 8: Open Science in a Changing Academic World by The Tortured Proteins DepartmentTopics:Compact for Academic Excellence in Higher EducationGovernment ShutdownHHMI's new open science policiesShrinking PhD poolsThe Nobel PrizesThe BearTLOS ReactionsPreprint: Experiment-guided AlphaF...

James Fraser reposted

Ben Barad
@baradlab.com

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!

James Fraser
@fraserlab.com

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

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.

James Fraser reposted

Andrew Ecker
@eckerchembio.bsky.social

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

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...

biorxiv.orgNinhydrin as a covalent warhead for chemical proteomic-enabled discovery and selective engagement of reactive argininesCovalent molecules have emerged as next-generation therapeutics and as powerful tools for perturbing fundamental biological processes. Chemical proteomic methods to screen for reactive proteinaceous a...

James Fraser reposted

Richard Sever
@richardsever.bsky.social

Replying to @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