I want to make the docking between a ligand and a receptor (G protein-coupled receptor) which functions in the monomeric state or in the dimeric state (homodimeric or heterodimeric). Knowing that in the homodimeric state, the formation of the complex requires specific alpha-helices of GPCRs, is there a specific tool (software or server)? Thank you for your answers
Rafik
You might want to look at this paper: Article Interfaces Between Alpha-helical Integral Membrane Proteins:...
I assume that "requires specific alpha helices" can be expressed as a positional constraint. Meaning residue X has to be near to these helices, or maybe even "theses helices have to be at the interface between the proteins".
If so you can incorporate that by writing down positional constraints in a constraint file and do protein - protein docking with Rosetta's Docking Protocol.
https://www.rosettacommons.org/docs/latest/application_documentation/docking/docking-protocol#constraints
You just need to add the -constraints:cst_file flag followed by the path to the constraint file.
The constraint file is just a text file where the constraints are written down like this:
AtomPair CA 1 CA 2 GAUSSIANFUNC 0 2 TAG
AtomPair CA 2 CA 3 GAUSSIANFUNC 0 2 TAG
AtomPair CA 2 CA 1 GAUSSIANFUNC 0 12 TAG
....
(with constraining only on the C-alpha atoms here).
Benjamin E. Mayer my sincere thanks for your help ! I will see your proposal and I will come back to you for questions if necessary.
regards,
Rafik