Hello,
I'm trying to write an script to calculate if two proteins interact.
I've found a lot of scripts but any of it is useful for me.
What I have is:
For each of my interactions that have a common pdb code I have a dictionary of each of the pdb codes as keys and a list with the different chains that are common to both parts of the interaction as value.
something like this:
Interaction_A = {4PKH:['F', 'D', 'A', 'I'] ,3B63:['A', 'C', 'B', 'E', 'D', 'G', 'F', 'I', 'H', 'K', 'J', 'M', 'L', 'N'] ,1YXQ:['B', 'A']}
Interaction_B = {4PKH:['F', 'D'] ,3B63:['A', 'C', 'B', 'J', 'M', 'L', 'N'] ,1YXQ:['B', 'A']}
The pdb files compressed in a directory similar to that:
/pk/pdb4pkh.ent.Z /b6/pdb3b63.ent.Z ...
And i dont know how to handle these files
The pdb have both proteins inside in different chains
What I want is to know is:
For each of the interactions, for each of the pdb and for each of the possible combinations between chains of the same pdb I want to know if any pair of chains have an atomic contact (if they interact)
I was thinking in use the python module Bio.PDB but it's almost no information on how to use it and I'm completely lost.
If someone can help me.
