Assume I have two proteins that have known tertiary structures. Is there a way that I can load these two proteins in pyrosetta, make some restraints between residues of these two proteins, and then use gradient descent to minimize the cost function in order to predict the interaction (based on constructed constraints) between these two proteins? If yes, could you please explain or provide me with some resources? I’m completely new to pyrosetta.
If they are already at the binding site in the crystal structure, you can use the MinMover or FastRelax to miniminize, or minimize/pack side chains. Contraints are also available in what ever way you want to. Some of those are covered in the PyRosetta notebooks tutorials: https://github.com/RosettaCommons/PyRosetta.notebooks If they are monomers and you are trying to get the best orientation between them, you want docking with constraints.
.
