I have a dimeric protein which I want to model. I want to enforce a two-fold symmetry between the subunits, and I also want to enforce a particular alignment to the template I've selected. I've considered a couple options for encoding this:
1. Create a 3D Format restraint file for a monomer and submit to I-TASSER. Afterwards, reconstruct the dimer of the model based on the symmetry axis in the template structure. The problem is that I-TASSER will not consider the interface, which could potentially change the model
2. Submit to COTH/SPRING/TACOS/another co-threader, which can handle the protein interface properly. However, non of the server interfaces have options for specifying restraints, which are essential for this application. I'd rather not have to install anything, but if it is possible to specify restraints on the command line of one of these co-threaders, I'd be willing to try.
Are there other approaches that would be better?
Thanks, Spencer