Rachel Seongeun Kim

The paper predicts quaternary structures of viral proteins using AlphaFold2 and AlphaFold-Multimer, identifying new insights into vaccinology and protease targets.

5,776,417 ColabFold-AlphaFold2 structures cover 98.9% of viral UniProt 2025_03 sequences, 16.4-fold more than earlier versions, with 75.3% high-confidence and 72.6% of viral reference proteomes fully covered.

Foldseek-Interface clusters protein interaction interfaces from PDB data, revealing 77,167 interface clusters and novel interface types.

Folddisco efficiently searches for similar protein structural motifs in large databases using a geometric feature index and rarity-based scoring, achieving faster query times and better storage efficiency than existing methods.

Phold pairs ProstT5-predicted 3Di tokens with Foldseek searches against 1,363,704 curated phage structures, annotating 49.4% of CDS in 1,419 INPHARED genomes versus 34.7% for Pharokka MMseqs2.

BFVD provides a large repository of predicted viral protein structures, enhancing annotation of bacteriophage proteins compared to sequence-based methods.