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).
(A) has no known natural ligands.
(A) has one known inhibitor (I) binding to (AE)
The structure of (AE) bound to (I) is available from PDB.
How do we identify which protein in (B) binds to (AE).
The obvious solution is to dock all proteins with known structures in
(B) to all known pockets in AE. Any better solutions?