AI systems have recently had a lot of success in one key aspect of biology: the relationship between a protein’s structure and its function. These efforts have included the ability to predict the structure of most proteins and to design proteins structured so that they perform useful functions. But all of these efforts are focused on the proteins and amino acids that build them.
But biology doesn’t generate new proteins at that level. Instead, changes have to take place at the nucleic acid level before eventually making their presence felt at the protein level. And the DNA level is fairly removed from proteins, with lots of critical non-coding sequences, redundancy, and a fair degree of flexibility. It’s not necessarily obvious that learning the organization of a genome would help an AI system figure out how to make functional proteins.
But it now seems like using bacterial genomes for the training can help develop a system that can predict proteins, some of which don’t look like anything we’ve ever seen before.
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