Design

Dear all,

can I used sequence_tolerance to optimize the binding pocket on a protein for a chemical compounds?

I used molfile_to_params.py to generate a params file for the compound. But I do not know how to feed this to sequence_tolerance?

Thank you for the help.

Hi,

I'm using pepspec to design a peptide. I've been able to run the application with some options (listed below) but my peptides always seem to fly off into space, with the exception of the region near the anchor residue. I've tried a few different combinations by looking at the application documentation, but I can't seem to get anything that looks "reasonable". My options are:

-pepspec::soft_wts soft_rep.wts

-pepspec::interface_cutoff 5
-pepspec::clash_cutoff 5.0

Hi,

I am trying to run the protein-RNA interface design protocol present in rosetta_demos. I found that in the xml file the residues that are allowed for design are not present in the protein (1a9n_ABQ). Am I missing something here ??

I also want to know whether rosetta can score protein-RNA interactions well or not, and what extra terms are scored in calculating the binding energy of the designed interface in case of protein-RNA interactions?

Hello,

In my version of PyRosetta, which I downloaded in december 2014, the mutate_residue function doesn't mutate the sequence of the Pose...

Here is the relevant part of my code:

for j in sequence:
(...)
mutate_residue(pose,resn,j, pack_scorefxn=score_fxn)
(...)
jd.output_decoy(pose)

When I do this, pose doesn't change even though its whole sequence should be replaced.