RefSeq virus protein structure prediction database

# Custom Virus database

A custom foldseek target database was created, including all protein sequences derived from plant-infecting viruses currently found in the NCBI RefSeq database. In total, 8,191 protein sequences were extracted and used as template for protein structure predictions.

Colabfold v1.5.2 (using localcolabfold), which is based upon AlphaFold v2.3.1(40), was used for protein model prediction. Setting: --random-seed 101 --num-seeds 3 --use-dropout --num-models 1 --num-recycle 8 --recycle-early-stop-tolerance 0.5

No templates were used during the protein model prediction. The uniref30_2302 and colabfold_envdb_202108 databases were used to generate the multiple sequence alignments (https://colabfold.mmseqs.com/)

The predicted structures were filtered based on the pLDDT value, resulting in a set of 7545 protein structures with a pLDDT ≥ 50.

## Files

modelling_stats.txt < Tab seperated file containing the modelling statistics for each structure prediction

pdb_files/all < folder containing all pdb files resulting from the structure prediction

pdb_files/pLDDT50 < folder containing all pdb files resulting from the structure prediction having a pLDDT score of 50 or higher

VIRAL_PROTEIN_PLANT_REFSEQ.fasta < fasta file contain all protein sequences extracted from plant infecting viral genomes uploaded in the NCBI RefSeq database