Google DeepMind’s Groundbreaking AI for Protein Structure Can Now Model DNA

Google spent much of the past year hustling to build its Gemini chatbot to counter ChatGPT, pitching it as a multifunctional AI assistant that can help with work tasks or the digital chores of personal life. More quietly, the company has been working to enhance a more specialized artificial intelligence tool that is already a must-have for some scientists.

AlphaFold, software developed by Google’s DeepMind AI unit to predict the 3D structure of proteins, has received a significant upgrade. It can now model other molecules of biological importance, including DNA, and the interactions between antibodies produced by the immune system and the molecules of disease organisms. DeepMind added those new capabilities to AlphaFold 3 in part through borrowing techniques from AI image generators.

“This is a big advance for us,” Demis Hassabis, CEO of Google DeepMind, told WIRED ahead of Wednesday’s publication of a paper on AlphaFold 3 in the science journal Nature. “This is exactly what you need for drug discovery: You need to see how a small molecule is going to bind to a drug, how strongly, and also what else it might bind to.”

AlphaFold 3 can model large molecules such as DNA and RNA, which carry genetic code, but also much smaller entities, including metal ions. It can predict with high accuracy how these different molecules will interact with one another, Google’s research paper claims.

The software was developed by Google DeepMind and Isomorphic labs, a sibling company under parent Alphabet working on AI for biotech that is also led by Hassabis. In January, Isomorphic Labs announced that it would work with Eli Lilly and Novartis on drug development.

AlphaFold 3 will be made available via the cloud for outside researchers to access for free, but DeepMind is not releasing the software as open source the way it did for earlier versions of AlphaFold. John Jumper, who leads the Google DeepMind team working on the software, says it could help provide a deeper understanding of how proteins interact and work with DNA inside the body. “How do proteins respond to DNA damage; how do they find, repair it?” Jumper says. “We can start to answer these questions.”

Understanding protein structures used to require painstaking work using electron microscopes and a technique called x-ray crystallography. Several years ago, academic research groups began testing whether deep learning, the technique at the heart of many recent AI advances, could predict the shape of proteins simply from their constituent amino acids, by learning from structures that had been experimentally verified.

In 2018, Google DeepMind revealed it was working on AI software called AlphaFold to accurately predict the shape of proteins. In 2020, AlphaFold 2 produced results accurate enough to set off a storm of excitement in molecular biology. A year later, the company released an open source version of AlphaFold for anyone to use, along with 350,000 predicted protein structures, including for almost every protein known to exist in the human body. In 2022 the company released more than 2 million protein structures.

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