Co-founder, CEO of Talus Bio structure-free discovery for frontier drugs

Seattle, WA
Joined December 2008
Do we even need to fold proteins at all to find drugs? Or do we just do that to satisfy our 3D brains? Meet Ptarmigan-1 🧵 - Structure-free drug discovery - 5000x less compute than co-folding - Finds known and cryptic pockets - Actually works on poorly structured targets
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Today we’re opening our structure-free AI drug discovery model for all to use! Ptarmigan-1 predicts which small molecules bind a protein, and where, without building a 3D protein structure. It learns from multiple kinds of data, including measurements of proteins at work inside living human cells. This is the culmination of a long and winding path to get here In my first week of grad school, I sat in a lecture hall where generations of chemists had trained and Nobel Prizes hung on display. One of the most accomplished chemists in the world introduced us to the word “undruggable,” describing targets that so many had given up on. I remember sitting there feeling so indignant. Of course all targets are impossible to drug until the right technology lets you drug it. Thankfully I found my people in @jaybradner's lab, where the T-shirts said “nothing is undruggable”, and got to work We focused on gene regulators there, proteins that control which genes turn on and off and can drive cancer. Most are poorly structured, making them difficult targets for traditional tech that focus on a well-defined binding pocket. Gene regulators are not the only disordered proteins though. Roughly 40% of the human proteome has significant disorder, and these targets remain out of reach while discovery for structured proteins gets faster every year. With Ptarmigan-1, we’re giving researchers a way to search for molecules against these targets without first having to solve their structure. I’m grateful to the team and supporters that brought us here. Now we get to see what the community does with it. Try it and tell us what you think. Link below.
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Well in my hands the bio filters have a 100% false positive rate, but I'm no statistician 🤷‍♂️
Today, we'll resume charging for requests our safeguards block before Claude responds. This only applies in categories with low false positive rates: biology, distillation attacks, and frontier LLM development. We've seen some coordinated attacks on our systems in recent weeks, and this is one layer of defense. In recent testing, 99.7% of accounts using Claude Code, Claude​.ai, or Cowork did not hit any of these newly "billable blocks." The classifiers behind the blocks we’re resuming charging for today are tuned to have a <0.1% false positive rate. We know that's not 0%, and we're going to keep improving them so they interrupt your work less often. If you think a request has been blocked incorrectly, please report it with /feedback in Claude Code. platform.claude.com/docs/en/…
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A molecule for every target that needs one
We’re hearing two kinds of voices on the potential of AI to cure all disease: One says AI will cure everything, but without a concrete path to get there. The other says biology is too complex to ever tame, but underestimates the power of the tools that will unlock the full potential of frontier intelligence. At Manifold Bio, we see a path and we’re already building it: a high-throughput interface into living system biology. Millions of protein designs, measured directly in vivo, to learn how molecules behave in the body and ultimately predict what they’ll do before they reach a patient. Today we share mBER-2, the latest iteration of our AI protein design model that is a core piece of this mission.
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Alex Federation retweeted
We’re hearing two kinds of voices on the potential of AI to cure all disease: One says AI will cure everything, but without a concrete path to get there. The other says biology is too complex to ever tame, but underestimates the power of the tools that will unlock the full potential of frontier intelligence. At Manifold Bio, we see a path and we’re already building it: a high-throughput interface into living system biology. Millions of protein designs, measured directly in vivo, to learn how molecules behave in the body and ultimately predict what they’ll do before they reach a patient. Today we share mBER-2, the latest iteration of our AI protein design model that is a core piece of this mission.
Today, we’re announcing mBER-2, our latest AI protein design system, and sharing a bit of how we use it to explore biology in vivo at scale. For a long time, we’ve been working on what I think of as “frontier problems” in medicine and biology. We know a lot about the targets involved in disease, but there is still an enormous amount of biology we haven’t explored, and potential uses for that biology we haven’t discovered. One of those problems is drug delivery. There are thousands of potential targets, and most receptors remain unexplored as routes for delivering medicines. We want to understand which ones we can use, where they can take a drug, and what kinds of molecules make that possible. Ultimately, we need to test these molecules in vivo to understand what they actually do. We’ve spent the last six years building measurement technologies that let us generate millions of measurements in living systems. mBER-2 is an AI protein design system built for that scale of in vivo measurement. Our goal is to generate binders across the full range of targets we care about, while systematically exploring the possible binding sites on each one. It’s not just what you bind, but where and how you bind that determines whether a molecule performs it's function. mBER-2 lets us probe those differences at massive scale. We’re also sharing a look at some of our in vivo data. We’ve designed more than 50 million molecules across over 4,000 targets, and screened millions of molecules in living systems. By probing hundreds of receptors, we’ve found new pathways for delivering genetic medicines into fat that outperform industry benchmarks by a large margin. This is just the beginning. We call the space of all bindable sites across proteomes the EpiTome. As we explore it, we’re building the data to connect AI design, receptor binding, and what a molecule actually does in a living organism. Much like the idea of a virtual cell, we envision a Virtual Organism that helps us design medicines with specific properties in mind. The foundation is our own in vivo data, connecting molecular design to outcomes measured in living systems. The endgame is to use AI to explore more biology, measure what happens, and use what we learn to design better medicines. Every round should deepen our understanding of biology and improve our ability to build molecules that do what we need them to do.
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Alex Federation retweeted
This is fun. 1. Mango Banana - banana on the outside, mango on the inside. Enough said. 2. Plant machine interfaces - we should be able to trade plants N,P,H2O for reduced carbon compounds. Do to them what they did to chloroplasts 3. Solution phase self assembly of 3D memory chips using designed self-assembly of macromolecules - do we really get protein design 4. A brain the size of a building. - what would it be thinking? 5. A five assed monkey - bc South Park 6. Self growing housing - the rent is too damn high 7. Obviously brain machine interfaces - I will judge this by when I can browse the web by thinking about it. 8. Dinosaurs. 9. Cats with dog personalities. 10. A nice smelling microbiome
In light of the progress in mathematics, we at Edison Scientific and FutureHouse have assembled a set of Millennium Problems for Biology. They are chosen to be very hard to solve but very easy to validate in a simple laboratory environment. Any of these, if solved, would mark a major advance in biotechnology, and most of them would contribute materially towards curing disease. These are, in some sense, the “last reasonable eval” for AI in biology. This was work primarily by @MichaelaThinks and myself, with contributions from many others. Short descriptions below. The full descriptions of the problems with acceptance criteria are at the Bio Millennium Problems website, linked in the next post. Share more if you have ideas. If they meet our criteria, we’ll add them to our list (with attribution and permission).
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Alex Federation retweeted
1/ What could we discover if we had a binder for every protein in the human proteome? We are excited to introduce the Bindome, an open and free resource of over 300,000 designed protein binder candidates against over 8,000 human target proteins. 🧵
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Alex Federation retweeted
When you actually look at global biotech companies, the number of interesting molecules is very thin. Discovery and early stage has been disregarded for so long because of the biotech bear market. In the end, the funnel has to be better broadly distributed and early stage assets/novel targets are where the big wins are at. Both for patients and profits. $XBI
Discussion w the senior BD leaders at big pharma and one surprising point made is that more than one said that they are focused on earlier stage and are comfortable with clinical risk. They don’t seem to be shaken up by avidity/$NVS recent post deal setback. “In BD, risk is your friend. If you don’t take risk. You’ll pay what others think it’s worth” talking about transacting phase 2 or earlier, pre readout $XBI $IBB
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Alex Federation retweeted
I've attempted to map everything in oncology in a public website and open source repo for all. The site is trying to get all cancers, products, technologies, bottlenecks, people, startup opportunities with 1000+ ideas for upgrading the field. If you have a loved one with cancer and you are technical or can engineer, go take a look, file improvement requests or bugs or help with the open repo and make this the best open and free info resource for individuals, researchers and educational use. This should save people time, aid AI oncology projects and generate positive action. If you are not technical just complain in this thread about broken or annoying or things you want and I'll fix them live. Some of the interesting pages: Treatments: onco.cc/drugs A gallery of the molecules being used onco.cc/molecules/ And targets: onco.cc/targets/ The technologies in oncology: onco.cc/technologies/ 1100 ideas for helping oncology: onco.cc/ideas/ Bottlenecks on oncology: onco.cc/bottlenecks/ Open questions (LETS GO RESEARCH PEOPLE) onco.cc/open-questions/ Startup requests (LETS GO STARTUP PEOPLE) onco.cc/startup-requests/ Mechanics of cancer: onco.cc/mechanics Battlefronts: onco.cc/fronts/ Isotope supply: onco.cc/isotopes Key papers: onco.cc/key-papers Pipeline funnels: onco.cc/pipeline Cancer by type: onco.cc/cancers/ Institutional rankings: onco.cc/institutions/ The startups: onco.cc/startups/ Heros and heroines : onco.cc/heroes/ Key medical people: onco.cc/people/ Here is the project roadmap: onco.cc/roadmap/ Models and data sets: onco.cc/models/ There are other views as well, take a browse. Try making a PR if you have an upgrade to this on the repo here: github.com/judegomila/OnCo If you are biologically/medically minded and something is wrong, file a bug as well or say on the thread and we will get it fixed live. If this is a useful project star the repo and help get it calibrated. I've tried to add some other languages but I cannot speak them so tell me if that doesnt work well. I believe we will crack oncology and having total information dominance is key to the problem. Let the feedback flow!
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Unlocking 0-to-1 targets won't fix clinical decision making on its own What it does is open territory that was completely inaccessible before Our job is to hand trialists genuine first-in-class molecules instead of wasting patient populations on the 15th me-too for the latest hot target xitter.cf/biogerontology/status/…
Bender, Scannell, Shaywitz and colleagues in NRDD: a decade of AI in drug discovery, clinically relevant impact still limited. Their fix is right. Stop benchmarking model accuracy; benchmark whether the tool changes a real Go/No-Go. We proved translation is possible with Rentosertib. nature.com/articles/s41573-0…
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Alex Federation retweeted
Every tech VC wants to believe that drug discovery is now a function of compute. They think if we throw enough H100s at the problem, tokenize enough dead sequences, and scale virtual cells, biology will be 'solved'. They are wrong. Drug discovery is not a function of compute. It is a function of measurement.
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Beautiful articulation of how hard targets actually get unlocked throughout history Build new tech to generate new fit-for-purpose data, push through with persistence and luck, and now leverage the data with AI to broaden the approach. The targets at the frontier keep changing, the technology keeps changing, but thankfully for patients the curve is accelerating xitter.cf/srikosuri/status/20998…
Today, there's a strong focus on fast-follows of existing drugs. The drug programs that inspire me look different – the target is known, but we don't know how to build the drug, often requiring the dev of new tech that paves the path for more drugs.
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If we're still in the fun part of the scaling law for protein structure... imagine where we are for structure-free discovery. Lots of low-hanging gains to be made, just need the right data
Five pharma companies just fine-tuned OpenFold3 in a federated setting on 20,000+ structures... ... raising correct ligand-pose predictions from 29% to 47%
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Alex Federation retweeted
Five pharma companies just fine-tuned OpenFold3 in a federated setting on 20,000+ structures... ... raising correct ligand-pose predictions from 29% to 47%
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Alex Federation retweeted
the moat isn't the model anymore, it's the data nobody else has
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Faster co-folding gives marginal gains for the same old targets. Dropping folding unlocks new targets that were previously impossible, and insane speed. We screened every protein vs 3B compounds in a single day.
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Alex Federation retweeted
Every so often, a major event happens in your life to validate years of work. SRRK’s ISEMBYLD was FDA approved. Having participated in its development from basic science to approval, as a physician-scientist, this is one of my best days. Happy for ISEMBYLD to help SMA patients.
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Alex Federation retweeted
while 95% of my feed is sloppy RPGs made by Astra I'm burning my all credits into understand how to fight aging and death
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Alex Federation retweeted
We raised a $40M Series A to build the automated lab for agentic biology. Last week, we shared the work we did with @Anthropic: Claude designed proteins, sent them to our automated wet lab, and got real experimental data back. We believe this is where biology is going: AI agents designing experiments, running them in automated wet labs, learning from the results and iterating. But AI can only move as fast as the experiments behind it. To use the potential of AI to cure all diseases, we need to build high-throughput wet lab infrastructure: a “biological gigafactory”. That’s exactly what we’re doing at Adaptyv. Over the past year we’ve grown our lab throughput by over 5x and onboarded more than 100 customers, ranging from bio AI labs like @chaidiscovery and @boltz_bio to pharmas like @Roche and @novonordisk to dozens and dozens of new startups that use AI to radically speed up drug discovery.
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