Retrieve PDB 2 uniprot mappings, with residue resolution
- python (either version 2 or 3)
Simply provide a list of PDB identifiers, lowercase
and one for each line, in the pdb_list.txt file. Then run:
bash prepare_commands.sh > commands.txt
parallel --jobs 1 --progress < commands.txt
echo -e "pdb id\tpdb chain\tpdb residue\tpdb position\tuniprot id\tuniprot residue\tuniprot position" > pdb2uniprot.tsv
find out/ -type f -name '*tsv' -exec cat {} >> pdb2uniprot.tsv \;
The pdb2uniprot.tsv file should look something like this:
pdb id pdb chain pdb residue pdb position uniprot id uniprot residue uniprot position
192l A M 1 P00720 M 1
192l A N 2 P00720 N 2
192l A I 3 P00720 I 3
192l A F 4 P00720 F 4
192l A E 5 P00720 E 5
192l A M 6 P00720 M 6
192l A L 7 P00720 L 7
192l A R 8 P00720 R 8
192l A I 9 P00720 I 9
The conversion is based on the SIFTS database (http://www.ebi.ac.uk/pdbe/docs/sifts/), to which we are very grateful
Copyright (C) <2016> EMBL-European Bioinformatics Institute
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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