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

“You know, as we mentioned, like I think at the very beginning is the goal with the product has been to, you know, address what the models don’t on their own.”

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Speaker unverified
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belief
Recorded
12 Feb 2026
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Latent Space

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…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. So I would say that the way that we structure kind of some of those validations was on the one end, we have validations across a whole set of different problems that, you know, the biologists that we were working with came to us with. So we were trying to. For example, in some of the experiments, design peptides that would target the RACC, which is a target that is involved in metabolism. And we had, you know, a number of other applications where we were trying to design, you know, peptides or other modalities against some other therapeutic relevant targets. We designed some proteins to bind small molecules. And then some of the other testing that we did was really trying to get like a more broader sense. So how does the model work, especially when tested, you know, on somewhat generalization? So one of the things that, you know, we found with the field was that a lot of the validation, especially outside of the validation that was on specific problems, was done on targets that have a lot of, you know, known interactions in the training data. And so it’s always a bit hard to understand, you know, how much are these models really just regurgitating kind of what they’ve seen or trying to imitate. What they’ve seen in the training data versus, you know, really be able to design new proteins. And so one of the experiments that we did was to take nine targets from the PDB, filtering to things where there is no known interaction in the PDB. So basically the model has never seen kind of this particular protein bound or a similar protein bound to another protein. So there is no way that. The model from its training set can sort of like say, okay, I’m just going to kind of tweak something and just imitate this particular kind of interaction. And so we took those nine proteins. We worked with adaptive CRO and basically tested, you know, 15 mini proteins and 15 nanobodies against each one of them. And the very cool thing that we saw was that on two thirds of those targets, we were able to, from this 15 design, get nanomolar binders, nanomolar, roughly speaking, just a measure of, you know, how strongly kind of the interaction is, roughly speaking, kind of like a nanomolar binder is approximately the kind of binding strength or binding that you need for a therapeutic. Yeah. So maybe switching directions a bit. Bolt’s lab was just announced this week or was it last week? Yeah. This is like your. First, I guess, product, if that’s if you want to call it that. Can you talk about what Bolt’s lab is and yeah, you know, what you hope that people take away from this? Yeah. Yeah. This is like your. First, I guess, product, if that’s if you want to call it that. Can you talk about what Bolt’s lab is and yeah, you know, what you hope that people take away from this? Yeah. You know, as we mentioned, like I think at the very beginning is the goal with the product has been to, you know, address what the models don’t on their own. And there’s largely sort of two categories there. I’ll split it in three. The first one. It’s one thing to predict, you know, a single interaction, for example, like a single structure. It’s another to like, you know, very effectively search a space, a design space to produce something of value. What we found, like sort of building on this product is that there’s a lot of steps involved, you know, in that there’s certainly need to like, you know, accompany the user through, you know, one of those steps, for example, is like, you know, the creation of the target itself. You know, how do we make sure that the model has like a good enough understanding of the target? So we can like design something and there’s all sorts of tricks, you know, that you can do to improve like a particular, you know, structure prediction. And so that’s sort of like, you know, the first stage. And then there’s like this stage of like, you know, designing and searching the space efficiently. You know, for something like BullsGen, for example, like you, you know, you design many things and then you rank them, for example, for small molecule process, a little bit more complicated. We actually need to also make sure that the molecules are synthesizable. And so the way we do that is that, you know, we have a generative model that learns. To use like appropriate building blocks such that, you know, it can design within a space that we know is like synthesizable. And so there’s like, you know, this whole pipeline really of different models involved in being able to design a molecule. And so that’s been sort of like the first thing we call them agents. We have a protein agent and we have a small molecule design agents. And that’s really like at the core of like what powers, you know, the BullsLab platform. So these agents, are they like a language model wrapper or they’re just like your models and you’re just calling them agents? A lot. Yeah. Because they, they, they sort of perform a function on behalf of. hese agents, are they like a language model wrapper or they’re just like your models and you’re just calling them agents? A lot. Yeah. Because they, they, they sort of perform a function on behalf of. They’re more of like a, you know, a recipe, if you wish. And I think we use that term sort of because of, you know, sort of the complex pipelining and automation, you know, that goes into like all this plumbing. So that’s the first part of the product. The second part is the infrastructure. You know, we need to be able to do this at very large scale for any one, you know, group that’s doing a design campaign. Let’s say you’re designing, you know, I’d say a hundred thousand possible candidates. Right. To find the good one that is, you know, a very large amount of compute, you know, for small molecules, it’s on the order of like a few seconds per designs for proteins can be a bit longer. And so, you know, ideally you want to do that in parallel, otherwise it’s going to take you weeks. And so, you know, we’ve put a lot of effort into like, you know, our ability to have a GPU fleet that allows any one user, you know, to be able to do this kind of like large parallel search. So you’re amortizing the cost over your users. Exactly. Exactly. And, you know, to some degree, like it’s whether you. Use 10,000 GPUs for like, you know, a minute is the same cost as using, you know, one GPUs for God knows how long. Right. So you might as well try to parallelize if you can. So, you know, a lot of work has gone, has gone into that, making it very robust, you know, so that we can have like a lot of people on the platform doing that at the same time. And the third one is, is the interface and the interface comes in, in two shapes. One is in form of an API and that’s, you know, really suited for companies that want to integrate, you know, these pipelines, these agents.…

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