Still, Verba’s team uses AlphaFold (both 2 and 3, because they have different strengths, he says) to run virtual versions of their experiments before running them in the lab. Using AlphaFold’s results, they can narrow down the focus of an experiment—or decide that it’s not worth doing.
It can really save time, he says: “It hasn’t really replaced any experiments, but it’s augmented them quite a bit.”
New wave
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.”
Genesis Molecular AI is pushing margins of error down from less than two angstroms, the de facto industry standard set by AlphaFold, to less than one angstrom—one 10-millionth of a millimeter, or the width of a single hydrogen atom.
“Small errors can be catastrophic for predicting how well a drug will actually bind to its target,” says Michael LeVine, vice president of modeling and simulation at the firm. That’s because chemical forces that interact at one angstrom can stop doing so at two. “It can go from ‘They will never interact’ to ‘They will,’” he says.
With so much activity in this space, how soon should we expect new types of drugs to hit the market? Jumper is pragmatic. Protein structure prediction is just one step of many, he says: “This was not the only problem in biology. It’s not like we were one protein structure away from curing any diseases.”
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