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.
Best,
Rhonald
Hi Rhonald,
I am very new to Rosetta and PyRosetta. But I just had some experience on alanine scanning via PyRosetta.
On the webpage of Pyrosetta (http://pyrosetta.org/scripts.html), you should be able to find the sample PyRosetta code (Alanine-scanning and ddG calculation) done by Sid Chaudhury. It will give you the idea.
I asked the same question about specifying environment-dependent H-bond in the scoring function to the MiniRosetta mailing list. Based on the feedback, it seems not possible now to make the exact scoring function in MiniRosetta or PyRosetta as the terms introduced in the PNAS paper. If you want the exact same H-bond weights in the scoring function, Robetta is the only choice.
However, I was also told that the "environmental weights" were somehow "smoothed" from 0.2 for fully-exposed hydrogen-bonding pairs to 1.0 for fully-buried hydrogen bonding pairs, and will be active if you the "score12" score function. I think Liz Kellogg has already used this in her ddg protocol of MiniRosetta to predict the globular protein stability after mutation. But it seems no benchmarks are available regarding to the interface ddg (binding affinities of alanine scanning).
I hope these information will be helpful.
Thanks,
Jianqing
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.