BFVD v3-UniProt-complete, improved viral protein structure predictions

The Big Fantastic Virus Database (BFVD) v3 is the most comprehensive resource for ColabFold-AlphaFold2-predicted viral protein structures. It holds 5,776,417 structures of nearly all viral sequences in UniProt 2025_03, a 16.4-fold increase compared to the representative-only catalogs of BFVD v1 and v2. Structure prediction quality has also improved, with high-confidence predictions accounting for 75.3% of BFVD v3 entries. This is due to Logan's enormous sequence assembly, now mined for the entire BFVD v3 instead of only for shallow alignments, alongside continued prediction quality improvements. BFVD v3 covers 72.7% of ICTV's virus species, 1.54-fold more than BFVD v2. With this version, the fraction of fully covered viral reference proteomes increases from 1.5% to 72.6%. BFVD v3 thus brings us closer to a structural catalog of the known virosphere and is freely available at bfvd.steineggerlab.workers.dev and bfvd.foldseek.com.