new blogpost: Nasal sprays and peptides for virus protection blog.booleanbiotech.com/nasal-sprays...

I wrote a primer on AI antibody design, published on Asimov press. www.asimov.press/p/antibody-d...

How to Design Antibodies

A step-by-step guide to making de novo binders.

asimov.press

Check out our new review on binder discovery! In a fast-moving world, here are some thoughts we have in the moment. Congrats @jzy2799.bsky.social and Eddy!! www.sciencedirect.com/science/arti...

Toward universal binder discovery: Advances in display, computational design and in vivo platforms

Protein binders are fundamental tools in chemical biology, key components of biotechnologies, and the foundation of biologics-based medicines. However…

sciencedirect.com

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...

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

Developability comes for free...?

Did AI de novo antibody generation models learn developability properties without explicitly being trained on this?

ayusuf.substack.com

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...

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...

Tudor-Stefan Cotet (@CotetTudor) / X

Tudor-Stefan Cotet (@CotetTudor) / X

x.com

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!

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...

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.

github.com

I wrote up a short blogpost on using Claude Code / Opus 4.5 for computational biology blog.booleanbiotech.com/claude-code-...

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!

Hannes Stark@hannes-stark.bsky.social · 9mo ago

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

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...

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...

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 🧵

Diego del Alamo@delalamo.xyz · last yr.

Apparently this tendency of PLMs to cut and paste across multiple sequnces during de novo design mimics what we see in natural sequences. Not sure what to make of it yet