I analyzed binding pockets across X-ray structures within a protein family and aligned them based on their structure. Now I would like to compare the pockets to make a statement about structural conservation of these pockets. For this, I would like to measure the distances between the centers, so that I can create a matrix of pairwise distances of each pocket and then cluster them. I am new to python/biopython and only know how to measure distances between single residues in different proteins in pymol, but this would take forever to do it for 60 structures with an avereage of 8 pockets per protein. Is there a way in biopython to approach this? The pocket centers are defined as heteroatoms in a different chain than the protein (protein = chainA; pockets = chainZ).
Any kind of help is appreciated!