I want to dock 2 membrane proteins that the structure is lacking the transmembrane domain (TMD), I only have the extracellular domains but I know which way the protein faces the membrane.
How do I restrain the docking so it will be take into account this restriction?
I am using the web server
Dear Karen
There is no simple way of doing. One option would be to define a planar shape constituting of fake beads and define a few restraints from residues of your protein that you know to face the membrane to those beads. E.g.
assi (segid A and resi XX) (segid S) 0.0 0.0 0.0
where XX is the residue number of the amino acid facing the membrane. You should define for each of your proteins a few of those restraints.
The “shape” should be uploaded to the server as shape, with segid defined as S. Not that with a single layer, you might end up with proteins on both side depending on what is the information you have to drive the docking of your two proteins.
I am attaching here an example of such a shape (PDB file).
planar-shape.pdb (9.7 KB)
Give it a try (if still needed).