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Symmetry

optimisation of a protein-protein interface

Category: 
Design
Scoring
Symmetry

Dear Rosetta users,

I have a symmetrical homo-dimeric structure for which I would like to select a single point mutation that will increase the affinity between the monomers. I thought about design&relax protocol, in which one position is designed while the remaining ones are only allowed to repack. Such a protocol would be used to scan all the interface positions.

My questions is how to set up this in Rosetta Scripts? Perhaps there are easier/better ways to do this?

Thanks for help! Staszek

Post Situation: 

mr_protocols with symmetry and ligand

Category: 
Symmetry

Hello,

I have been trying to use mr_protocols on a homologous pdb into a cryo-em density. When I run the protocol with symmetry and without the ligand it works properly. The trouble comes when I try to include a ligand. The resulting pdb is does not contain the ligand. This is the mr_protocol that I have submitted:

#####################################################

#!/bin/bash

Post Situation: 

How to transform a pose from symmetric into non-symmetric?

Category: 
Design
Scoring
Constraints
Symmetry

Hello,

Is there a way to break the symmtery of a pose in the middle of a Rosetta script? I want to avoid writing the PDBs and feeding them again to a new script.

Any suggestion is highly appreciated!

Thanks!

Post Situation: 

symmetric design in the presence of a nonsymmetric ligand

Category: 
Design
Symmetry
Small Molecules

Hello,

I am trying to design a C3 symmetrical protein with a ligand bound at the C3 interface. What is the best way around this in RosettaScripts? I was thinking to first symmetrize the pose with SetupForSymmetry and then add the ligand with AddChain mover. But it seams, SetupForSymmetry is not compatible with extra_res. As soon as the script arrives at SetupForSymmetry, it throws the following error:

Post Situation: 

dock & design

Category: 
Docking
Design
Constraints
Symmetry

Dear All,

I would like to simultaneously dock and design two (or more) identical subunits into a a symmetric homooligomer.

Input:

- backbone structure of a monomer (no sidechains!);
- initial arrangement of the subunits;
- constraints that precisely define interactions between the subunits.

Simulation:

Post Situation: 

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