2024/10/28 by Rachel Seongeun Kim, Eli Levy Karin, Milot Mirdita +2 · 2 voices · 4 citations
Environmental Science · Biochemistry, Genetics and Molecular Biology · #Bacteriophages and microbial interactions #Genomics and Phylogenetic Studies #RNA and protein synthesis mechanisms
paper · pdf · doi:10.1093/nar/gkae1119
openalex publication_date 2024/10/28 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite providing predictions for over 214 million UniProt entries, the AFDB does not cover viral sequences, severely limiting their study. To address this, we created the Big Fantastic Virus Database (BFVD), a repository of 351 242 protein structures predicted by applying ColabFold to the viral sequence representatives of the UniRef30 clusters. By utilizing homology searches across two petabases of assembled sequencing data, we improved 36% of these structure predictions beyond ColabFold's initial results. BFVD holds a unique repertoire of protein structures as over 62% of its entries show no or low structural similarity to existing repositories. We demonstrate how a substantial fraction of bacteriophage proteins, which remained unannotated based on their sequences, can be matched with similar structures from BFVD. In that, BFVD is on par with the AFDB, while holding nearly three orders of magnitude fewer structures. BFVD is an important virus-specific expansion to protein structure repositories, offering new opportunities to advance viral research. BFVD can be freely downloaded at bfvd.steineggerlab.workers.dev and queried using Foldseek and UniProt labels at bfvd.foldseek.com.