This GitHub repository is for making the Pfam seeds structure database (PfamSDB) by cutting the related full-length structures on their domain borders.
Prerequisites:
- python
- pandas
- Numpy
- gsutil (It is assumed that you have access to the Alphafold database)
- GNU parallel
This script was run on a machine with SLURM job scheduler. It uses job arrays to download structures and cut them in parallel.
It can be executed as follows:
cd scripts
batch=32 #We will cut structures in batches. You can specify the number of batches here.
bash Prepare2DownloadStructs.sh $batch
sbatch --array=1-$batch DownloadTarStructsAndExtractFasta.sh
bash Prepare2ChopStructs.sh
sbatch --array=1-$batch RunCifChopper.sh
python Concat_ChoppedAndRemoveExtra.py
The PfamSDB will be inside the structures directory.