I am working with some protein that has 6 polar basic residues on its binding site. I would like to find similar proteins on PDB (or other database) that have this type of residues (polar basic residues (ARG or LYS or HIS)) at similar 3D positions (given some threshold). It would be something similar to ligand pharmacophore similarity search, but for parts of proteins. How can I perform this query?
PS: Given the unavailability of such software, I am thinking about developing a GPU based software that would scan whole PDB database for finding related proteins given user's input. If somebody is interested, we could collaborate. This is serious, please contact me.