This AI Software Nearly Predicted Omicron’s Tricky Structure
On November 26, the World Health Organization designated the strain of coronavirus surging in South Africa a “variant of concern” and christened it Omicron. The next day, University of British Columbia professor Sriram Subramaniam downloaded a genome sequence posted online and ordered samples of Omicron DNA to be shipped to his lab.
Subramaniam’s group uses electron microscopes to reveal the 3D structure of proteins, to better understand how they work. It had already mapped the spike proteins that coronaviruses use to bind and enter human cells for some earlier strains. Describing Omicron’s spike protein felt urgent because its DNA differed in ways that might explain the variant’s rapid spread. But like others doing online shopping that weekend, Subramaniam had to be patient: Until the DNA arrived in the mail, he couldn’t put Omicron proteins under the microscope.
Across the continent, University of North Carolina at Charlotte computational genomics researcher Colby Ford had also been thinking about Omicron’s spike protein. Relatives had been asking him a question also troubling many experts: Would Omicron evade existing vaccines? Those vaccines teach the body to respond to spike proteins from an earlier strain. Instead of ordering lab supplies, Ford tried a recently invented shortcut. On the same day WHO christened Omicron, he used free artificial intelligence software to try and predict the structure from the sequence of amino acids encoded in Omicron’s genome.
In about an hour, Ford got his first results, and quickly posted them online. Early in December, he and two colleagues posted a fuller paper, now accepted for publication, including predictions that some antibodies to previous strains would be less effective against Omicron.
Subramaniam’s lab received its Omicron DNA soon after and published its microscope observations of the structure along with results from tests of real antibodies on December 21. One of Ford’s two predicted structures proved to be pretty much right: He calculated that the positions of its central atoms differ by around half an angstrom, about the radius of a hydrogen atom. “These tools allow you to make an educated guess really quickly—which is important in a situation like Covid,” Ford says. “With any new virus that comes along, someone else will replicate what I did here.”
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January 10, 2022 at 04:09AM