I have been using STRING to generate interacting partners of a specific protein. (based on this post).
In the graphical version when for example for protein O15357 , I perform the search I can see the network and I am able to generate the PDB Codes of the interacting partners for those which have a structure.
Now I need to use the STRING API and for generating the interacting partners for O15357, I simply use:
But this one only returns the Ensembl Id (e.g. .ENSP00000275493) of the interacting partners.
When I use the command below, I can retrieve the pdbcodes but I do not understand the format:
http://string.embl.de/api/psi-mi/interactionsList?identifiers=O15357&required_score=400&limit=20
Do you have any suggestion how to generate the pdb codes? is it possible to generate pdb code for Ensembl Ids?
thanks in advance.
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what do you mean with "I don't understand the format" ? http://string.embl.de/api/psi-mi/interactionsList?identifiers=O15357&required_score=400&limit=20 is just an XML file. It clearly contains some PDB identifiers e.g: 1wcp ( http://www.rcsb.org/pdb/files/1wcp.pdb )
I do understand it is XML file, the problem is that there are several PDB codes while in the graphical version for the same query I get less PdbCodes. So the main problem is how to interpret these pdbCodes.