I want to perform a molecular docking between a protein of interest and several ligands. This membrane protein has a transmembrane domain composed of an alpha helix structure, which exerts it's function in a dimeric conformation, that is, by binding two identical proteins in its transmembrane domain. The crystal structure for this protein it's not available so it is necessary to design it ab initio. For this, we have the following working protocol:
Design of the monomeric 3D structure from the amino acid chain. FMAP software.
Obtaining the percentage of protein embedded in the membrane and its degrees of tilt. OMP.
Design of the dimeric structure. RosettaMP
Exploratory simulations for the selection and refinement of the dimeric model. CHARMM-GUI
The main problem I'm finding with this approach is that Rosetta software needs supercomputing capacity. I would like to know if there's a reliable server option for developting the dimeric structure.