Brian Naughton

Excellent, comprehensive rundown of the state of bio lab automation by @owlposting1.bsky.social

In retrospect, it's an important topic that has had almost zero discussion over the years!

A fun surprise to see some decade-old(!) work show up in there too.

www.owlposting.com/p/heuristics...

Developability comes for free...? Did AI de novo antibody generation models learn developability properties without explicitly being trained on this?

Great piece on antibody developability in the AI era by Adil Yusuf
ayusuf.substack.com/p/developabi...

github.com/adaptyvbio/p...

Very cool Claude skills for protein design from x.com/CotetTudor and Adaptyv.

Their standard pipeline should enable anyone (+Claude) to easily design binders at close to state of the art!

I'm happy to see it uses my biomodals repo in parts github.com/hgbrian/biom...

Tudor-Stefan Cotet (@CotetTudor) / X Tudor-Stefan Cotet (@CotetTudor) / X

Very cool Claude skills for protein design from x.com/CotetTudor and Adaptyv.

Their standard pipeline should enable anyone (+Claude) to easily design binders at close to state of the art!

I'm also happy to see it uses my biomodals repo in parts github.com/hgbrian/biom...

~180 lines of code to win the in silico portion of the Adaptyv Nipah binding competition Here's the script we used to get 1st place in the in silico portion of the Adaptyv Nipah competition: import modal def download_boltz2(): from mosaic.models.boltz2 import Boltz2 Boltz2() ...

finally wrote up some notes on the adaptyv competition: blog.escalante.bio/180-lines-of....

Blogpost: I took an oral probiotic for a month and did microbiome sequencing at @Plasmidsaurus.

blog.booleanbiotech.com/oral-microbi...

Releasing alignism, a small tool that I have found useful for doing multiple sequence alignment in browser.

hgbrian.github.io/alignism/

- The hard work was done by the awesome biowasm team!
- Does tree building too
- V fast compared to e.g., muscle on EBI
- Not tested that much!

Great! If each student signs up for modal you'd get $$$ in free compute.

GitHub - hgbrian/foldism: protein folding app running on modal protein folding app running on modal. Contribute to hgbrian/foldism development by creating an account on GitHub.

I semi-vibe coded a frontend for all the protein folding tools I've been running. It runs on modal and has 5 different open-source algorithms: Chai1, Boltz2, AF2, Protenix(-mini).

Not 100% polished but hopefully of use to some use to people in the field!
github.com/hgbrian/fold...

I wrote up a short blogpost on using Claude Code / Opus 4.5 for computational biology

blog.booleanbiotech.com/claude-code-...

I was conserving characters but Sally Smith Hughes wrote “Genentech: The Beginnings of Biotech”

A treasure trove of biotech and early SV oral histories by Sally Hughes: digicoll.lib.berkeley.edu/search?p=%28...

Genentech (Boyer, Goeddel (recommended!)), VC (Byers, Rock, Valentine), Kaiser ("History of the Kaiser Permanente Medical Care Program"), Lilly, Paul Berg, Stan Cohen, lots more.

I’ve been testing BoltzGen a bit recently and while I haven’t done any experimental testing yet, the quality of the software is very clear. It installs, runs, logs everything, has tons of options. Very excited to test out the designs irl!

I decided to experiment with my own (small) protein design competition!

It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.

You submit a modal script, I run it and test on benchbb.bio

blog.booleanbiotech.com/vhh-competit...

Pretty interesting that AFAICT the filtering was done after the fact (so, library 1 had no filtering). This could make it an excellent dataset for training/testing filters/rankers. Too bad it looks like the dataset is not public

Another promising VHH model just dropped today from Manifold Bio. This one builds on BindCraft and ColabDesign. MIT license!

www.biorxiv.org/content/10.1...

The success rates appear to be lower than other tools, but this is highly target-dependent.

New blogpost on the latest in AI antibody design.

Including some code to easily run Germinal and IgGM on modal!

blog.booleanbiotech.com/ai-antibody-...

It has been interesting to use gitingest to paste entire codebases for new tools into Gemini and ask for severe bugs (logic, incorrect variables...).

I think it found at least one this morning. I have to double-check before filing but it's a real bug from what I can tell...

In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.

Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.

A REALLY nice use of nanobanana (Gemini) is cleaning up blurry old images. Of course it depends what you ask for, but it is amazing at keeping the text and content the same.

We decided to try to 3d print custom chess pieces.

The workflow of asking gemini to iterate on a design image, then uploading that image to adam.new worked amazingly well. 5 minutes work!

Left is the gemini image and right is the mesh.

I was reminded about Blackett's War by a mention on the @patio11 podcast. Terrific book about operations research / probability theory applied to real world problems.

Lots of anecdotes like this...

Recently tested some de-novo minibinders against two targets (thanks Adaptyv!) designed using our open-source design library, `mosaic`; our best method got hit rates of 7/10 and 8/10 and affinities as low as single-digit nanomolar. Wrote up some thoughts here: blog.escalante.bio/minibinder-d...

Ibex from Prescient Design arxiv.org/abs/2507.09054 github.com/prescient-de...

- antibody folding with performance like Boltz/Chai but up to 100X faster
- does not fold the complex, just the antibody
- predicts holo and apo forms
- sadly, model weights are not freely available

Now that OpenCRISPR is in nature and rekindled the 'what's-a-novel-sequence' debate, I'm happy to share an app to check this, which I built for fun some time ago.

fuerstlab.shinyapps.io/SeqNovelty/

quick 🧵

After many months heads down, we at Decade are growing! We are hiring a protein biochemist to help us radically improve cancer treatment.

If you like being early and making an impact, we are interested to hear from you! Details here: decade.bio/careers

Asking Claude to research binder designs metrics and it gave me my own blogpost back!

Time to start writing for the AIs? marginalrevolution.com/marginalrevo...

The Failures and Futures of Cancer Vaccines The cancer vaccine field has yet to become a systematic science despite decades of work and a steadily rising number of clinical trials since the first clinical PoC a decade ago.  A core problem faci...

Great article on cancer vaccines by @mackenziejem.bsky.social
www.mackenziemorehead.com/the-failures...

Vibe coded a run progress simulator with Gemini Canvas.

It worked great, until the context rot doom loop set in, and now it's difficult to fix the remaining minor bugs.

Still very impressive!

hgbrian.github.io/run_progress...

It's not too hard, though benchmark.py has too much (AI) code

- add an entry to the yaml file
- add image1.txt through image6.txt to that output dir
- run benchmark.py

I would still manually check. There are cases where >1 answer is acceptable, especially the header can be ambiguous