The Big Fantastic Virus Database v3 is the most comprehensive resource for ColabFold-AlphaFold2-predicted viral protein structures, bringing us closer to a structural catalog of the known virosphere and is freely available at bfvd.workers.dev and bfvd.foldseek.com.
Abstract
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.
Mechanistic understanding of viral protein-protein interactions enables global health security and pandemic preparedness, yet experimental characterisation remains difficult, costly, and often restricted to specialised laboratories. Here, we describe an in silico campaign using AlphaFold2 and AlphaFold-Multimer to pred...
Yew-On Han, Riya Narain, Razan Abbara et al.· bioRxiv· 0 citations
Significance Currently, there exists a huge gap between the number of available viral coat protein (CP) sequences and the experimentally determined capsid structures. Moreover, there are no resources available that provide full capsid models. By leveraging the observation that CP tertiary structures and their capsid or...
Oscar Rojas Labra, David S. Montoya-Munoz, Nelly Santoyo-Rivera et al.· Proceedings of the National...· 1 citation
Zika virus is a mosquito-borne flavivirus that caused a major epidemic in the Americas in 2015 and 2016 and is associated with congenital birth defects and neurological disease. Like other flaviviruses, it depends on conserved sequence and RNA structural elements that carry out essential steps in its life cycle and in...
Emma B. Dickinson, Eric P. Nawrocki· bioRxiv· 0 citations
The results establish Sma3s v3 as a scalable and interpretable tool for functional annotation and re-annotation of proteomes, pangenomes, and metagenomic protein catalogues.
Alejandro Rubio, Jesús L. García-Junco Alcalá, Elisa Luque-Jiménez et al.· bioRxiv· 0 citations
Retrieving BGCs related to those of a known producer can be regarded as a representation-learning objective. We hypothesize that ESM-2 sequence-derived representations of BGCs can improve retrieval beyond the Pfam-domain content metric. Our toolkit is the following: group-disjoint train, validation, and test assignment...
Rustambek Urokov, Asifullah Khan, Farhod Eshboyev et al.· bioRxiv· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
