RefSeq virus protein structure prediction database

<p dir="ltr"># Custom Virus database </p><p dir="ltr">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. </p><p dir="ltr">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</p><p dir="ltr">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/)</p><p dir="ltr">The predicted structures were filtered based on the pLDDT value, resulting in a set of 7545 protein structures with a pLDDT ≥ 50.</p><p><br></p><p dir="ltr">## Files</p><p dir="ltr">modelling_stats.txt < Tab seperated file containing the modelling statistics for each structure prediction</p><p dir="ltr">pdb_files/all < folder containing all pdb files resulting from the structure prediction</p><p dir="ltr">pdb_files/pLDDT50 < folder containing all pdb files resulting from the structure prediction having a pLDDT score of 50 or higher</p><p dir="ltr">VIRAL_PROTEIN_PLANT_REFSEQ.fasta < fasta file contain all protein sequences extracted from plant infecting viral genomes uploaded in the NCBI RefSeq database</p>