Viro3D Dataset – Part 1: Metadata, ColabFold Predictions and Foldseek database

This repository contains Part 1 of the dataset associated with the manuscript “Viro3D: a comprehensive database of virus protein structure predictions” by Ulad Litvin, Spyros Lytras, Alexander Jack, David L. Robertson, Joseph Hughes, and Joe Grove.

The dataset includes:

• Metadata: protein and species lists in CSV format (viro3d_metadata.tar.gz)

• Relaxed ColabFold predictions in PDB format (colabfold_pdb.tar.gz)

• ColabFold pLDDT and pTM confidence scores in JSON format (colabfold_json_scores.tar.gz)

• ColabFold multiple sequence alignments in A3M format (colabfold_msa.tar.gz)

• Viro3D Foldseek structural search database (foldseekViro3D.tar.gz)

• Foldseek-derived structural protein clusters (viro3d_protein_clusters.tar.gz)

• Foldseek-derived structural similarity network (viro3d_protein_network.tar.gz)

• Foldseek-based annotation expansion of protein functions (viro3d_annotation_expansion.tar.gz)