I've recently started to use the Rosetta suite for some basic modeling of an orphan GPCR. Our research group has discovered several compounds that interact with the membrane protein, either directly or indirectly. To see if any of these compounds could act as ligand, I turend to the ligand-dockng protocol. I went through the tutorial (with some issues) however the results were succesful. Now that I am trying to do it with my orphan GPCR, i've run into some issues:
It seems that the tutorial uses a crystal_complex file of the crystallized structure of the receptor and antagonist to score the models, as well to align the antagonist to the binding pocket. My orphan receptor has no crystallized strucure, however I have a decent predicted model. I do not know where the ligands could possibly dock to so my questions are:
(1) Can I still use this protocol to predict potential protein-ligand interaction without a known crystallized strucure, and if so;
(2) How would I proceed to try and model these protein-ligand interactions?
I'm very new to this with just basic terminal/python knowledge, so I apologize if my questions are too basic.
Thanks in advance,
You are here
Ligand Docking with Orphan GPCR