esm.doi.bio/esm3/esm3.discussion.full1

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We have found that language models can reach a design space of proteins that is distant from the space explored by natural evolution, and generate functional proteins that would take evolution hundreds of millions of years to discover. Protein language models do not explicitly work within the physical constraints of evolution, but instead can implicitly construct a model of the multitude of potential paths evolution could have followed.

language models evolution protein design space functional proteins physical constraints model

Proteins can be seen as existing within an organized space where each protein is neighbored by every other that is one mutational event away (54). The structure of evolution appears as a network within this space, connecting all proteins by the paths that evolution can take between them. The paths that evolution can follow are the ones by which each protein transforms into the next without the collective loss of function of the system it is a part of.