Pipeline for analyzing Domain-Cofactor interaction patterns using PDB and ECOD
git clone https://github.com/chrisBioInf/PECODER/
cd PECODER
(You will need, at a minimum, a functioning Pandas and Biopython installation in your Python PATH)
1.) Get the ECOD reference data base:
cd ECOD
sh download_ecod_tsv.sh 291
cd ..
(you can replace the 291 with any version number you want)
2.) Get a Cofactor -> PDB ID mapping from PDBsum:
curl https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/data/lig2pdb.lst > lig2pdb.txt
3.) Download PDB crystal structures corresponding to some Cofactor (here: COA):
python download_from_PDB.py -f lig2pdb.txt -o PDB COA
4.) Scan and annotate atom-level interactions with PECODER:
mkdir -p Results
python PECODER.py --ecod ECOD/ecod_domains291.tsv --pdb PDB -o Results -c COA