THERE’LL BE TIME ENOUGH FOR COUNTING:
What’s next for AlphaFold: A conversation with a Google DeepMind Nobel laureate: “I’ll be shocked if we don’t see more and more LLM impact on science,” says John Jumper (Will Douglas Heaven, November 24, 2025, MIT Technology Review)
Proteins are made from strings of amino acids that chemical forces twist up into complex knots. An untwisted string gives few clues about the structure it will form. In theory, most proteins could take on an astronomical number of possible shapes. The task is to predict the correct one.
Jumper and his team built AlphaFold 2 using a type of neural network called a transformer, the same technology that underpins large language models. Transformers are very good at paying attention to specific parts of a larger puzzle.
But Jumper puts a lot of the success down to making a prototype model that they could test quickly. “We got a system that would give wrong answers at incredible speed,” he says. “That made it easy to start becoming very adventurous with the ideas you try.”
They stuffed the neural network with as much information about protein structures as they could, such as how proteins across certain species have evolved similar shapes. And it worked even better than they expected. “We were sure we had made a breakthrough,” says Jumper. “We were sure that this was an incredible advance in ideas.”What he hadn’t foreseen was that researchers would download his software and start using it straight away for so many different things. Normally, it’s the thing a few iterations down the line that has the real impact, once the kinks have been ironed out, he says: “I’ve been shocked at how responsibly scientists have used it, in terms of interpreting it, and using it in practice about as much as it should be trusted in my view, neither too much nor too little.” […]
AlphaFold was designed to be used for a range of purposes. Now multiple startups and university labs are building on its success to develop a new wave of tools more tailored to drug discovery. This year, a collaboration between MIT researchers and the AI drug company Recursion produced a model called Boltz-2, which predicts not only the structure of proteins but also how well potential drug molecules will bind to their target.
Last month, the startup Genesis Molecular AI released another structure prediction model called Pearl, which the firm claims is more accurate than AlphaFold 3 for certain queries that are important for drug development. Pearl is interactive, so that drug developers can feed any additional data they may have to the model to guide its predictions.
AlphaFold was a major leap, but there’s more to do, says Evan Feinberg, Genesis Molecular AI’s CEO: “We’re still fundamentally innovating, just with a better starting point than before.”