I am working on a transmembrane protein which is a homologus trimer.Its crystal structure contains only the extracellular portion but not the transmembrane and intracellular portion. I need to model the missing transmembrane and intracellular domains. Does anyone know a pipeline in ROSETTA to do this job? I only know that the Rosetta application "helix_from_sequence" can create the structural model of a single transmembrane helix, but how to build the intracellular domain and assemble the modeled transmembrane region and the intracellular domain to the extracellular domain? How to ensure the correct contact among the three modeled transmembrane helixes and the correct orientation when doing the assembly?
Is there anyone know how to solve these problems? I will be very much grateful if you can help.
Thank you in advance.