Thanks for your useful replies. I have another relevant question. As I said, I need to consider alternative conformations of a given protein structure. Based on the energies of these conformations I want to decide whether a conformation is acceptable or not. A conformation C is acceptable if the probability of transition from the initial conformation (PDB structure) to conformation C is reasonable (the energy of conformation C is not much higher than the energy of initial conformation).
I use PyRosetta to compute the energies of conformations. My question is: what is an acceptable energy difference? In other words, what is a good choice for parameter alpha in the following statement: An alternative conformation C is acceptable if its energy is not more than alpha units higher than the energy of initial conformation.