Postdoc opportunity with Michel Goedert and myself to work on #cryoEM/#cryoET structures of #amyloids. Feel free to email me with any questions you might have. mrc.tal.net/vx/mobile-0/...

Bit belated, but our article on error analysis for MSMs is in JCTC! pubs.acs.org/doi/abs/10.1...

I'm giving a talk at One World Cryo EM (cryoem.world) tomorrow at 11:00am EST. Topic is 'Deconstructing Algorithms for “Discrete” Heterogeneity in Cryo-EM'. Sign up for their mailing list to tune in!

www.thecrimson.com/article/2025... ...and what's more, absolutely none of this happens in a vacuum. There's much I love about academia, but one thing I absolutely hate is the way it permits professors to abuse the power they have over their mentees. We have systemic issues we need to face.

We are hiring for a postdoc to work on the intersection of molecular simulation, machine learning, and cryo-EM! Please find the job posting here. thiedelab.github.io/docs/postdoc...

Faculty opening in Cornell Chemistry at the Assistant Professor level in the area of chemical biology, broadly defined! academicjobsonline.org/ajo/jobs/30338 #chemjobs

Back from our first group conference trip to ACS Fall. Was great to not only see new science, but also excellent watch the very excellent presentations from Josh (Rhodes), Diego, and Jeffrey, as well as the great reception Josh (Almonte)'s poster received!

Excellent read for anyone trying to understand what is up with all the AI hype nowadays.

Posting a job ad on behalf of Mat Sikora, who is doing some fascinating work on cryo-EM for glycans. He's looking both for PhDs and postdocs. science.phd.uj.edu.pl/join/biomedi...

Happy to see our first collaboration with the Yang group come through!

We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org. A great position for someone who is looking to be a tech for a few years before grad or med school. aprecruit.ucsf.edu/JPF05424

The Open Molecules 2025 dataset is out! With >100M gold-standard ωB97M-V/def2-TZVPD calcs of biomolecules, electrolytes, metal complexes, and small molecules, OMol is by far the largest, most diverse, and highest quality molecular DFT dataset for training MLIPs ever made 1/N

One of grants frozen at Cornell: $6.7M (4 yrs) to develop heart pumps for babies born w/ heart defects. It took decades of work to get to point of prepping device for in-human clinical trials. No private company could do this. The cruelty of the Trump administration is heartbreaking. So to speak.

Agreed: Universities are far too quick to ignore the words of the actual people in power, e.g. J.D. Vance saying, "Professors are the enemy" and "[Orban's seizure of universities is] the closest that conservatives have ever gotten to successfully dealing with leftwing domination of universities"

It is with great pleasure that I announce that the Thiede lab has solved the problem of interpretability in AI for Chemistry with our new neural network architecture: the Variational Alanine Encoder (VAE).

Wishing all the trans scientists out there who are continuing to do amazing work in adverse conditions a good trans day of visibility!

I think it has more to do with you might get locked up for absolutely no reason at all and then flown to El Salvador to die in prison even though a judge said you should be released

Our (SMBP + SMBP alumns) man doing us proud.

How I've been generating nice equations in google slides:

On Hanukkah, Jews participate in many ancient rituals such as helping their parents transfer files between computers.

Y'all better have been getting those finger exercises in because those dreidels ain't gonna spin themselves.

First little piece of funding for our new project direction joint with the Yang group: characterizing electrochemical situations with ML + in-situ EM. Congratulations to Yao for the successful proposal! news.cornell.edu/stories/2024...

An excellent point, and something that we run afoul of in far too many of our algorithms that boil down to "generalization of PCA / CCA in some conformational space".

It is obvious that the PDB is biased towards proteins that scientists are more interested in. Similarly, its structures appear to be biased towards more interesting regions of proteins. This preprint finds that ligand binding sites tend to be more carefully modeled than the rest of the structure.

Googles claim that their result "lends credence to the notion that quantum computation occurs in many parallel universes" is nonsense, because their results are perfectly well explained by quantum mechanics independent of how you interpret it. 4/5

ESM3 structure predictions for multimers seem to be broken: In our (preliminary) experiments, it seems to always predict chain breaks around one amino acid in length.

Spent the last day of class yesterday telling my students that orbitals don't actually exist and real electrons exist in indescribable many-electron wavefunctions. For my next trick I'm telling all my nephews and nieces that Santa isn't real.

Looking into condensates at ~1 nm resolution! www.biorxiv.org/content/10.1...

Been a while since I read a paper like this: • "What [DiffDock] appears to be doing cannot be considered" docking • "Results are ... contaminated with near neighbors to test cases" • "Results for DiffDock were artifactual" • "Results for other methods were incorrectly done" arxiv.org/abs/2412.02889

Interesting article on the limitations of Alphafold2. Thanks Diego!

Steps to add a collaborator to a Github repo: 1. Enter Github PW on Laptop 2. Receive 2FA code to be entered on Github App 3. Enter PW into Github App 4. Enter different 2FA code from authenticator app 5. Re-request 2FA code for laptap. 6. Enter new code into phone app. 7. Add the user. Oy.

What are people's favorite non-diffusion generative models for protein structure? I'm 2-3 years behind in the literature and want to get caught up.

Fascinating thread here: apparently, caffeine and ibuprofen both have binding affinity to their target proteins so weak that they might get tossed out of a typical drug discovery project!

Something that's come up in a few conversations and I think is underappreciated: the X-ray / cryo-EM structures you download from the PDB are average structures, but not *typical* structures: very few proteins in your sample actually look like that.

Checkout the latest work by our #MSKPostdoc @sukritsingh92.bsky.social

1.5 years in, and going from postdoc to assistant prof has been a bit of a let-down. I get far fewer opportunities to say, "If my calculations are correct."

Question for cryo-EM people on Bluesky. How would you describe the difference between discrete and continuous heterogeneity? Curious about people's perspectives / definitions / hot takes, not looking for one "right answer."

Continuing yesterdays rant about ML research code, I am back with another plea. Can we stop passing dictionaries around everywhere? Dictionaries are not self-documenting because I have to RUN the code in order to see what keys/values are in it. Dataclasses are almost always better. Use them pls 🙏