AlphaFold

“There is this, ah, a few papers that came out, one was in Cell, I think last year, which showed that for all of the claims about AlphaFold-solving drug discovery, people try to take AlphaFold-produced protein structures, use them for traditional docking, and f…”

“And I think of the prominent AI leaders, I think Demis does a pretty good job of actually Translating the technology into more quantifiable and tangible ways for, like, your every person, because I think there's a lot of focus on, like, benchmarks and a lot of…”

“I was told by some of my, you know, pharma executive friends that, you know, almost every drug Discovered from now on will have used alpha fold at some point in it, in the drug discovery process.”

“The lesson I've learned from all the alpha projects we've done, specifically alpha go and alpha fold is I think the techniques we have and the problems I look like to look for are great in, if this, if the situation can be described as massive combinatorial se…”

“One thing I can think see happening is Gemini, Claude, or one of these general systems making use of alpha fold, like specialized systems as tools. I don't think we're going to have it just in one giant brain because it will have too much regression in if I pu…”

“And when DeepMind's project was completed, the company gifted its results to science, allowing researchers all over the world to make free use of its discovery.”

“The challenge is that you have a lot more than 20 building blocks when it comes to materials and so there's lots of different ways to think about chemical bonding, and right now no potentials are really robustly encoding all of that bonding, especially with re…”

“So it's just hard to know from experiment or from other computations if these types of models are correct, and they're certainly not correct across all of chemical space and I'd say they could fail more catastrophically than AlphaFold obviously fails, though t…”

“You now have three and a half million researchers accessing it in over a 190 countries.”

“From this evolutionary information about potential contacts, Then it's almost as if the model is sort of running some kind of, you know, Diestro algorithm, where it's sort of decoding, okay, these have to be closed, okay, then if these are closed and this is c…”

“And it's been incredibly gratifying to see, you know, three million researchers around the world use it in their important research.”

“I think in future Almost every single drug that's discovered from now on will probably have used AlphaFold at some point in that process, which is, you know, amazing for us, and, you know, really, that's what we do, all the work we do for.”

“They end up getting 90% prediction accuracy, and they basically solve the single protein folding question.”

“They folded two hundred million plus, basically every known protein in existence, and they made it available.”

“If you're an entrepreneur, like forget building a GPT wrapper, build an alpha fold wrapper. I think you could build multi-billion dollar, like what Cursor did. Cursor basically said, they didn't make the model. They were like, we'll take Claude, but we'll just…”

“Part of what we're trying to unlock here with Biohub is the idea of what actually, what happens If you do frontier biology and frontier AI in sync together and you're designing the tools on the frontier biology side in order to specifically collect and be able…”

“I mean, we don't have less researchers working on proteins. We have actually have many more, right?”

“AlphaFold solved one of the hardest problems in in chemistry. A problem that had been open for years. Name a drug that's resulted from it. Not one.”

“Sort of where are the X-ray crystallographers who are displaced because of it, right? That was what X-ray crystallographers were doing only physically. They're not out of work. They're, in fact, there's more demand for them.”

“And I would say similarly with a virtual cell model, it may not tell me literally why, just like a alpha fold doesn't tell me literally why did the protein fold this way and how, but it just told me the end state and it was reasonably accurate. I think that wo…”

“So AlphaFold itself is a hybrid model where you have the learning component, this probabilistic component you're talking about, which is, you know, based on neural networks and transformers and things, and that's learning from the data you give it you know, an…”

“There about, I think, 35,000 citations of AlphaFold, but within that is there are tens of thousands of examples of people using our tools to do science that I couldn't do on my own.”

“It isn't about one idea. It's about many mid-scale ideas that add up to a transformative system, and it's very, very important when you're building these systems to think about what we would call in this context biological relevance.”

“And we had about a third of the error of any other group on this assessment.”

“One is that we open source the code and we actually open source the code about a week before we released a database of predictions starting originally at 300,000 predictions and later going to two hundred million. Essentially every protein from an organism who…”

“The tweet on the left from Yoshitaka Morawaki came out two days after our code was available. We had predicted the structure of individual proteins, but we considered, we were working on building a system that would predict how proteins came together. But, ah,…”

“I like to think that our work Made the whole field of what's called structural biology, biology that deals with structures, you know, five or 10% faster. But the amount to which that matters for the world is enormous.”

“I think we will start to see this on more general systems, be them LLMs or others, That we will find more and more scientific knowledge within them, and we'll use them for important, important purposes, and I think this is really where this is going, and I thi…”

“Where there wasn't actually enough real experimental data to build the final alpha fold, so we had to build an earlier version that then predicted about a million protein structures, and then we selected, it had a confidence level on that, we selected the top …”

“And also alpha fold is actually a neurosymbolic model, and it's probably the best thing that AI ever did.”

“I think that would be like maybe five years from now. Yeah. So I have a kind of five year project and a lot of the alpha fold, the old alpha fold team are working on that.”

“AI being applied to chemistry and biology, Particularly around protein folding and protein drug interactions and things like that really was a breakthrough. So I think that, that probably merits it.”

“And there have been literally dozens of companies that have been started since DeepMind was published, and probably several billion dollars of capital that's gone into companies that are creating new drugs, creating new industrial biotech applications, using t…”

“Progress in pharmaceuticals in particular is an area where I think we'll see very rapid progress. You know, I I've spent a lot of time there just personally, because it's an area that I find very interesting. There's been incredible advancements in biological …”

“And, you know, in many ways, all of the subsequent breakthroughs, whether they were learning to play Atari games or AlphaGo or AlphaFold or many of the health applications that we did that produced best in the world class of x-ray recognition or ophthalmology,…”

“We've used AlphaFold now to map all two hundred million proteins known to science, or two hundred million proteins known to science, and we've made that available to everyone.”

“That's part of the reason why we started the Alpha Fold project, because it was actually my group that was looking around for other applications of DQN-like, AlphaGo-like tools, and in a hackathon that we did one week someone stumbled across, across this probl…”

“I mean, Facebook released this kind of like rando version of alpha fold recently. It's not that good.”

“If CMS and Medicare go and really crunch those costs, what is pharma going to do? Well, pharma is going to do what is the obvious thing, which is like, if you're going to cap what I can make, I have to completely change my R and D model. And they're just going…”

“What this team at Harvard did that they published two weeks ago is a really groundbreaking, extremely detailed view of the entire nuclear comp, nuclear pore complex, Around the nucleus of the cell by combining both x-ray imaging and alpha fold.”

“This is an incredible example of how AlphaFold's been used to solve this really misunderstood or never really well understood aspect of biology that is at the root cause of so much of disease and creates all this opportunity for medicine and therapeutics, rese…”

“AlphaFold feels to me like what ARPANET was, which was the origins of the internet, you know back when it was first installed, and no one really Kind of grappled with the ramifications of what would emerge. And I think, you know, once we have the ability to de…”

“And the accuracy of their predictive model now is within the range of error of the microscopes that are being used to actually scan and measure those proteins.”

“It's an inevitability that in the next couple of 24 months, someone else will replicate this.”

“I think we're within, within one year, J. Cal, of a lot of startups replicating this alpha fold technique, and then using that to go do drug discovery, and you'll see 50 startups getting funded 12 to 18 months from now based on some novel protein idea.”

“And the output of that is going to be an incredible new tool for drug discovery that is going to extend human lifespan in an incredible way.”