You are here

Design

score:weights for fixbb application in Rosetta 3.5

Category: 
Design

Hi,

If you specify a weights file using the option '-score:weights' , will that weighted scoring function be used in optimizing side chain placement? That is, does the simulated annealing algorithm incorporate the scoring function specified by '-score:weights', or is 'score:weights' only used in the final scoring of the structure AFTER side chains are placed and the designed PDB is complete?

Thanks,
Tyler

Post Situation: 

Output fasta of enzdes generated pdbs

Category: 
Design

Hi everyone,

I am using enzyme design application to mutate my enzyme. How can I extract a list of the pdb name, residues and residue number from the output generated by Rosetta.

The sequence recovery does something similar, but i need to know what residues have changed in what position. I am looking for trends hence I need to do this fo a bunch of pdbs that meet my cut off. Is there a quick way of getting a series of fastA files that I can view on any sequence alignment tool or a table ?

Thanks in advance for your help

Post Situation: 

sequence_tolerance optimize the binding to chemical compounds

Category: 
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.

Post Situation: 

Minimization Issue: Coarse Graining to All atom modeling

Category: 
Docking
Design
Loop Modeling

Hi all,
I want to get an all atom model of my coarse grained protein structure (after adding all the side chains back). I have been using the repacking algorithm to do so, but unfortunately its not doing the job. The side chains are not packed properly. Can you help me suggesting on how to go from coarse grained protein to get an all atom model for my protein. Is there any minimization protocol that can take care of this. Kindly let me know.

Thank you.

Post Situation: 

Pepspec options

Category: 
Design

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

Post Situation: 

Re: Protein-RNA interface design

Category: 
Design
Nucleic Acids

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?

Post Situation: 

Can't append or prepend with pepspec

Category: 
Design

Hi there

I have the basic pepspec working nicely, but I'd like to try the options to append or prepend. My flags look like this

-database /home/daniel/progs/rosetta_2014.16.56682_bundle/main/database
-in:file:s best_relaxed.pdb
-o best_relaxed_append_test
#tips says basically use these
-ex1
-ex2
-extrachi_cutoff 0
-pepspec::n_peptides 1000
-pepspec::pep_chain D
-pepspec::pep_anchor 490

-pepspec::n_append 1

Post Situation: 

mutate_residue doesn't mutate

Category: 
Design

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.

Post Situation: 

References where Rosetta is used to compute ddG of binding after mutation?

Category: 
Design

Rosetta has some applications that can be used to setup a protocol to compute the ddG of binding upon mutation (relax, fixbb or ddg_monomer to create wt structure and mutated structure, InterfaceAnalyzer to compute binding energies, etc.) Are there references available where Rosetta is used this way? Until now I have found papers where the authors either fit their own energy function to experimental data (instead of using Rosetta's energy function), or they use other applications (molecular dynamics, for example) to relax their structures, or something else.

Post Situation: 

Pages

Subscribe to RSS - Design