2) To calculate dG(partner), the predicted change in protein stability of a monomer, how do I set the amino-acid type dependent reference energies? Will “Standard” work?
The standard score12 set is optimized for protein design. It is possible to reoptimize the set of reference weights for ddG of mutation, which might be more appropriate here; look up the work of Kellogg in the Baker lab.
3) Is the weight of the aa dependent backbone torsion angle propensity set by “rama”?
There are two terms here in score12. p_aa_pp give the propensity for a position to be a certain amino acid given its phi and psi; rama gives the propensity for a position to be a certain phi and psi given its amino acid type.