Protein-Protein Docking Problem.
I am looking for a solution to the following problem. Any insight will be greatly appreciated.
A membrane receptor (A) has an extracellular domain (AE), transmembrane domain (AT) and intracellular domain (AI).
A bacteria (B) binds to (AE) leading to dimerization of (A) at (AT) and subsequent downstream signaling through (AI).
The obvious solution is to dock all proteins with known structures in (B) to all known pockets in AE. Any better solutions?