Dear PyRosetta developers,
I have used the Robetta server in the past to obtain
ddG(bind) and dG(partner) values
for mutations X -> A, and
I wish to use PyRosetta to do something similar.
I have been using PyRosetta for one week, and
I have the following questions:
1) Is it possible to specify environment-dependent
H-bond weighting in the scoring function,
as in Kortemme and Baker, PNAS 2002 (22)14116-21
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?
3) Is the weight of the aa dependent backbone torsion angle propensity
set by "rama"?
My goal is to be able to reproduce the Robetta results,
or the 'correct' results. Thank you and I really look forward
to using your Python tools together with sequence analysis
to study protein-protein interfaces.