Calibrated structural homology transfer yields putative molecular functions for domains of unknown function in four model proteomes
Jodh Singh Pannu, Kendall Green, Jeffrey Vedanayagam
The paper evaluates functional annotation reliability from remote homology searches using retrospective DUFs and finds Foldseek performs better than MMseq2 but not significantly better than ESM-2 embeddings.
bioRxiv · Sep 16, 2026 · PreprintBioinformatics