I am attempting to dock a small peptide/protein onto human death receptors such as DR4 and DR5 in an attempt to see whether these small peptides/protein can bind to these receptors the same way death ligands do.
In literature, the biological ligands that bind to such receptors, death ligands, bind in a fashion that takes three such extracellular components of these receptors to form a trimeric complex. Three death receptors bind to a death ligand.
In docking, should I were to simulate the trimerization, would I consider three molecules of the same receptor plus the ligand, giving a total of 4 molecules in the Input Data tab of the webserver, and would I adjust the ‘Pair to active/passive selection set number(s)’ to just interact with the molecule number pertaining to the ligand that I want to dock? Say the receptors are Molecules 1, 2, and 3, while the ligand is 4. For Molecule 1, would I just set the ‘Pair to active/passive selection set number(s)’ to 4?
In addition, is it appropriate to enable Symmetry Constraints of C3 symmetry to the receptors that trimerize?
Thank you in advance!