AlphaFold3 to offer structure prediction via web browser

Google DeepMind, the artificial intelligence company behind the popular AlphaFold tool, has published the next generation of the application’s protein structure prediction software. The new tool can predict the structures and interactions of an array of molecules including nucleic acids, small-molecule ligands, and macromolecule modifications (Nature 2024, DOI: 10.1038/s41586-024-07487-w).”Every time I gave an AlphaFold2 talk . . . people would always ask me, That’s really good, but I have a DNA-binding protein. Could you just tell me how it binds the DNA?” John Jumper, a director at Google DeepMind, said during a press conference. Unlike past versions, AlphaFold3, which was codeveloped with drug company Isomorphic Labs and first announced in October, can tackle such interactions.

AlphaFold3 shares many capabilities with the recently published RoseTTAFold-All Atom model. Though it lacks RoseTTAFold’s ability to design new proteins, AlphaFold3 has one big advantage: a new web server with a simple interface that requires no coding by the user. It enables anyone with a Google account to input the name of a protein or nucleic acid and develop predictions for the structures of complexes it forms with other molecules.

During the press conference, Julien Bergeron, a biologist at King’s College London who helped test AlphaFold3, predicted, “Every structural biology and protein biochemistry research group in the world will immediately adopt this.”

Casual users beware: AlphaFold3 will predict the most likely structure of any combination of input molecules, whether or not they genuinely interact. According to Max Jaderberg, chief AI officer at Isomorphic, the model assigns low confidence scores to complexes that are not thought to occur in the real world. His team is working on ways to predict binding affinity, which would help identify specious interactions—and assist in Isomorphic’s drug design efforts.