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!