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12 Feb 2026 Latent Space 🔬Beyond AlphaFold: How Boltz is Open-Sourcing the Future of Drug Discovery

“General pattern, I think, in like in trying to design things that are smaller, you know, like it’s easier to manufacture at the same time, like that comes with like potentially other challenges, like maybe a little bit less selectivity than like if you have something that has like more hands, you know, but the yeah, there’s this big desire to, you know, try to design many proteins, nanobodies, small peptides, you know, that just are just great drug modalities.”

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12 Feb 2026
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Latent Space

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…r to what AlphaVol3 proposed, which is very scalable. And we can use that to design new proteins. Oh, interesting. Maybe a quick shout out to Hannes Stark on our team who like did all this work. Yeah. Yeah, that was a really cool idea. I mean, like looking at the paper and there’s this is like encoding or you just add a bunch of, I guess, kind of atoms, which can be anything, and then they get sort of rearranged and then basically plopped on top of each other so that and then that encodes what the amino acid is. And there’s sort of like a unique way of doing this. It was that was like such a really such a cool, fun idea. I think that idea was had existed before. Yeah, there were a couple of papers. Yeah, I had proposed this and and Hannes really took it to the large scale. In the paper, a lot of the paper for Boltz2Gen is dedicated to actually the validation of the model. In my opinion, all the people we basically talk about feel that this sort of like in the wet lab or whatever the appropriate, you know, sort of like in real world validation is the whole problem or not the whole problem, but a big giant part of the problem. So can you talk a little bit about the highlights? From there, that really because to me, the results are impressive, both from the perspective of the, you know, the model and also just the effort that went into the validation by a large team. lights? From there, that really because to me, the results are impressive, both from the perspective of the, you know, the model and also just the effort that went into the validation by a large team. First of all, I think I should start saying is that both when we were at MIT and Thomas Yacolas and Regina Barzillai’s lab, as well as at Boltz, you know, we are not a we’re not a biolab and, you know, we are not a therapeutic company. And so to some extent, you know, we were first forced to, you know, look outside of, you know, our group, our team to do the experimental validation. One of the things that really, Hannes, in the team pioneer was the idea, OK, can we go not only to, you know, maybe a specific group and, you know, trying to find a specific system and, you know, maybe overfit a bit to that system and trying to validate. But how can we test this model? So. Across a very wide variety of different settings so that, you know, anyone in the field and, you know, printing design is, you know, such a kind of wide task with all sorts of different applications from therapeutic to, you know, biosensors and many others that, you know, so can we get a validation that is kind of goes across many different tasks? And so he basically put together, you know, I think it was something like, you know, 25 different. You know, academic and industry labs that committed to, you know, testing some of the designs from the model and some of this testing is still ongoing and, you know, giving results kind of back to us in exchange for, you know, hopefully getting some, you know, new great sequences for their task. And he was able to, you know, coordinate this, you know, very wide set of, you know, scientists and already in the paper, I think we. Shared results from, I think, eight to 10 different labs kind of showing results from, you know, designing peptides, designing to target, you know, ordered proteins, peptides targeting disordered proteins, which are results, you know, of designing proteins that bind to small molecules, which are results of, you know, designing nanobodies and across a wide variety of different targets. And so that’s sort of like. That gave to the paper a lot of, you know, validation to the model, a lot of validation that was kind of wide. And so those would be therapeutics for those animals or are they relevant to humans as well? They’re relevant to humans as well. Obviously, you need to do some work into, quote unquote, humanizing them, making sure that, you know, they have the right characteristics to so they’re not toxic to humans and so on. There are some approved medicine in the market that are nanobodies. There’s a general. General pattern, I think, in like in trying to design things that are smaller, you know, like it’s easier to manufacture at the same time, like that comes with like potentially other challenges, like maybe a little bit less selectivity than like if you have something that has like more hands, you know, but the yeah, there’s this big desire to, you know, try to design many proteins, nanobodies, small peptides, you know, that just are just great drug modalities. ing that has like more hands, you know, but the yeah, there’s this big desire to, you know, try to design many proteins, nanobodies, small peptides, you know, that just are just great drug modalities. Okay. I think we were left off. We were talking about validation. Validation in the lab. And I was very excited about seeing like all the diverse validations that you’ve done. Can you go into some more detail about them? Yeah. Specific ones. Yeah. The nanobody one. I think we did. What was it? 15 targets. Is that correct? 14. 14 targets. Testing. So we typically the way this works is like we make a lot of designs. All right. On the order of like tens of thousands. And then we like rank them and we pick like the top. And in this case, and was 15 right for each target and then we like measure sort of like the success rates, both like how many targets we were able to get a binder for and then also like more generally, like out of all of the binders that we designed, how many actually proved to be good binders. Some of the other ones I think involved like, yeah, like we had a cool one where there was a small molecule or design a protein that binds to it. That has a lot of like interesting applications, you know, for example. Like Gabri mentioned, like biosensing and things like that, which is pretty cool. We had a disordered protein, I think you mentioned also. And yeah, I think some of those were some of the highlights. Yeah.…

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