Google DeepMind has released an improved version of its biology prediction tool, AlphaFold, that can predict the structures not only of proteins but of nearly all the elements of biological life.

It’s a development that could help accelerate drug discovery and other scientific research. The tool is currently being used to experiment with identifying everything from resilient crops to new vaccines. 

While the previous model, released in 2020, amazed the research community with its ability to predict proteins structures, researchers have been clamoring for the tool to handle more than just proteins. 

Now, DeepMind says, AlphaFold 3 can predict the structures of DNA, RNA, and molecules like ligands, which are essential to drug discovery. DeepMind says the tool provides a more nuanced and dynamic portrait of molecule interactions than anything previously available. 

“Biology is a dynamic system,” DeepMind CEO Demis Hassabis told reporters on a call. “Properties of biology emerge through the interactions between different molecules in the cell, and you can think about AlphaFold 3 as our first big sort of step toward [modeling] that.”

AlphaFold 2 helped us better map the human heart, model antimicrobial resistance, and identify the eggs of extinct birds, but we don’t yet know what advances AlphaFold 3 will bring. 

Mohammed AlQuraishi, an assistant professor of systems biology at Columbia University who is unaffiliated with DeepMind, thinks the new version of the model will be even better for drug discovery. “The AlphaFold 2 system only knew about amino acids, so it was of very limited utility for biopharma,” he says. “But now, the system can in principle predict where a drug binds a protein.”

Isomorphic Labs, a drug discovery spinoff of DeepMind, is already using the model for exactly that purpose, collaborating with pharmaceutical companies to try to develop new treatments for diseases, according to DeepMind. 

AlQuraishi says the release marks a big leap forward. But there are caveats.

“It makes the system much more general, and in particular for drug discovery purposes (in early-stage research), it’s far more useful now than AlphaFold 2,” he says. But as with most models, the impact of AlphaFold will depend on how accurate its predictions are. For some uses, AlphaFold 3 has double the success rate of similar leading models like RoseTTAFold. But for others, like protein-RNA interactions, AlQuraishi says it’s still very inaccurate. 

DeepMind says that depending on the interaction being modeled, accuracy can range from 40% to over 80%, and the model will let researchers know how confident it is in its prediction. With less accurate predictions, researchers have to use AlphaFold merely as a starting point before pursuing other methods. Regardless of these ranges in accuracy, if researchers are trying to take the first steps toward answering a question like which enzymes have the potential to break down the plastic in water bottles, it’s vastly more efficient to use a tool like AlphaFold than experimental techniques such as x-ray crystallography. 

A revamped model  

AlphaFold 3’s larger library of molecules and higher level of complexity required improvements to the underlying model architecture. So DeepMind turned to diffusion techniques, which AI researchers have been steadily improving in recent years and now power image and video generators like OpenAI’s DALL-E 2 and Sora. It works by training a model to start with a noisy image and then reduce that noise bit by bit until an accurate prediction emerges. That method allows AlphaFold 3 to handle a much larger set of inputs.

That marked “a big evolution from the previous model,” says John Jumper, director at Google DeepMind. “It really simplified the whole process of getting all these different atoms to work together.”

It also presented new risks. As the AlphaFold 3 paper details, the use of diffusion techniques made it possible for the model to hallucinate, or generate structures that look plausible but in reality could not exist. Researchers reduced that risk by adding more training data to the areas most prone to hallucination, though that doesn’t eliminate the problem completely. 

Restricted access

Part of AlphaFold 3’s impact will depend on how DeepMind divvies up access to the model. For AlphaFold 2, the company released the open-source code, allowing researchers to look under the hood to gain a better understanding of how it worked. It was also available for all purposes, including commercial use by drugmakers. For AlphaFold 3, Hassabis said, there are no current plans to release the full code. The company is instead releasing a public interface for the model called the AlphaFold Server, which imposes limitations on which molecules can be experimented with and can only be used for noncommercial purposes. DeepMind says the interface will lower the technical barrier and broaden the use of the tool to biologists who are less knowledgeable about this technology.

The new restrictions are significant, according to AlQuraishi. “The system’s main selling point—its ability to predict protein–small molecule interactions—is basically unavailable for public use,” he says. “It’s mostly a teaser at this point.”

​ Artificial intelligence – MIT Technology Review

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