Hello, what are the general guidelines for docking, when one of the protieins is a transmembrane and its partner is supposed to dock to the extracellular part (e.g. antibody or ligand)?
- I suppose that the transmembrane one should be relaxed using MPFastRelax, whereas the extracellular using the standard REF15?
- Which scoring function should be specified for docking?
- Should one include any constraint to hide the intracellular and membrane part from docking or it's not necesary?
- Are there any example protocols doing that?
Thank you in advance!
Post Situation:
I am interested in this topic too. An example xml file for docking a soluble protein to a transmembrane one will be helpful. Everything i have tried so far creates all sorts of errors.
The errors im getting from running the attached files are ,
ERROR: The SpanningTopology object in MembraneInfo is empty! and
ERROR: Cannot split pose by membrane jump! Quitting...
Thank you for helping out
I found a related thread https://www.rosettacommons.org/node/10446. Apparently docking a soluble protein to a TM one was not possible in 2020. Is it still the current status, or has there been any progress in the meantime?