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...

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...

I spent way too long on this but I made a small benchmark for OCR of biological sequences. It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works! github.com/hgbrian/bio_...

BindEnergyCraft claims to improve BindCraft performance using an energy-based objective. "Code will be released soon."

Clever mosquito detector, draws a circle around the mosquito so you can squash it. $200 bzigo.com

I have been copying some amino acid sequences out of PDFs and so far nothing (Gemini, Claude, ChatGPT) works at >99% accuracy. I have to manually inspect everything! Even when you can highlight the text in the PDF, it is very often wrong! Anyone know anything that works?

The inverse vaccine / tolerization stuff is amazing. Similar to peanut tolerization but for any autoimmune disease? www.theguardian.com/wellness/202...

new blogpost: AI and protein patents blog.booleanbiotech.com/ai-protein-p...

We have gotten some really good responses to science questions from platform.futurehouse.org already. Both from "Crow" (short answers) and "Falcon" (deep research). It looks like this is state of the art right now!

TIL you can add .txt to a biorxiv fulltext link and get plain text. Handy for pasting into LLMs, e.g., the new BindCraft revision www.biorxiv.org/content/10.1...

There are now a trio of great pieces covering the rapid rise of Chinese biotech: - atelfo.github.io/2024/12/20/w... - centuryofbio.com/p/commoditiz... - www.asimov.press/p/china-trials

Results are honestly fascinating and amusing. 1. It succeeded on my first test to identify the function of a protein sequence - it correctly ran BLAST and identified the function although got specific details wrong. It then hallucinated *wildly* about details (domains, active sites) 1/n

sciencemachine.ai looks really interesting (default example analysis below) I am not sure how uploading to the browser can work for real sequencing data though. Maybe they will take a bucket url or something.

I did not know @plasmidsaurus.bsky.social is doing eukaryote nanopore sequencing now. The price is good, especially $50 extra for extraction. Unfortunately you cannot yet send any tissue, only certain blood and cell culture.

Since BoltzDesign1 just got published, people might also be interested in github.com/escalante-bi... by @nboyd.bsky.social It has a nicely flexible system for including custom losses. It's also surprisingly little code on top of Boltz (and the Jaxified Joltz).

Super excited to share that our paper on a multi-modal cell-free RNA foundation model is out! A fantastic collaboration with @genophoria.bsky.social, @fhormozd.bsky.social and the @exai.bio team!

Checking into options for home lab testing. A lot of places are now offering the Tasso device or similar for home collection: - mylabsdirect.com/product/comp... - rythmhealth.com - siphoxhealth.com - www.functionhealth.com - www.walkinlab.com

interesting report on synbio in china by Zach Sun sepiabio.substack.com/p/observatio...

new blogpost on protein binder design blog.booleanbiotech.com/protein-bind...

Is there a plasmidsaurus for DNA assembly yet? Basically someone to quickly turn IDT oligos or Twist fragments into longer DNA fragments.

Running out of memory used to be a common headache when running molecular simulations with neural network potentials. Not any more. Here Orb is simulating over half a million atoms on a single GPU (H200). This is a fully solvated COVID spike protein. Models here: github.com/orbital-mate...

Excited to share what I’ve been working on with @tkaraletsos.bsky.social to transform the field of drug discovery with atomistic foundation simulation models! I could not be more thrilled to be working with this dream team. achira.ai

Kurzweil still takes Resveratrol??

Interesting case study: Spontaneous tumor regression following COVID-19 vaccination (2021) jitc.bmj.com/content/10/3...

new blogpost: A list of health-related products blog.booleanbiotech.com/health-relat...

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

Excerpt from "Parachute use to prevent death and major trauma when jumping from aircraft: randomized controlled trial", BMJ, 2018 pubmed.ncbi.nlm.nih.gov/30545967/

Intuitive Surgical is worth $200B, which I think would put it in the top 10 largest biotechs, bigger than Pfizer! companiesmarketcap.com/biotech/larg... This seems like a pretty interesting area for tech people looking at bio/health applications, compared to the default of drug development.

searching for pdb entries and google randomly did this

Ginkgo's AI client appears to be getting a bunch of updates. github.com/ginkgobiowor...

Since it's on HN, and a pain to search on amazon, here is heavy metal tested whey, collagen, creatine. Preferably in a bag, cheap, with more explicit testing. There may be better but these are reasonable. www.amazon.com/AGN-Roots-Pr... www.amazon.com/Premium-Coll... www.amazon.com/Pure-Creatin...

This excerpt from the new @owl_posting article reminded me of an interesting wikipedia page. "2. Extended half-life: Antibodies stay in your bloodstream for weeks vs < 1 day for small molecules. This means less frequent dosing."

Impressive claims from the recent EvolveX paper www.biorxiv.org/content/10.1... unfortunately it relies on a commercial tool, FoldX, so it's hard to test out

Nice writeup on plasticlist.org and other plastic news from @sprague www.personalscience.com/p/personal-s...

new blogpost: What we learned about binder design from the Adaptyv competition blog.booleanbiotech.com/what-we-lear...

Does this tool exist: - upload a library of pdfs - get emails recommending new papers from pubmed with the same themes

ColabSaprot is really very impressive... Fine-tune a state-of-the-art protein language model by just uploading a csv of proteins and values. colab.research.google.com/github/westl... Or download other people's models from huggingface.co/SaProtHub