MSA-based structure prediction models can be retrained as pathogenicity prediction models by upweighting BERT losses

Summary

MSA-based structure prediction models can be retrained as pathogenicity prediction models by upweighting BERT losses (1). AlphaMissense was retrained from scratch mostly using the AlphaFold2 architecture this way.

1.

Cheng J, Novati G, Pan J, Bycroft C, Žemgulytė A, Applebaum T, et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science. 2023;381(6664). Available from: https://doi.org/10.1126/science.adg7492