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Design

Ddg filter threshold value?

Category: 
Design

I am doing protein-protein interface design using RosettaScripts, and in the .xml file under the demo at:

ROSETTAPATH/demos/public/rosetta_scripts_pp-interfacedesign/scripts

It has the following line:

<Ddg name="ddG" scorefxn="talaris2014" threshold="-15" repeats="2"/> binding energy calculation; an average of two repeats is computed for better numerical accuracy

 

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What is interface_cutoff_distance? And why did my residues outside this value get designed?

Category: 
Design

Under the description for the mover RepackMinimize:(https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/RepackMinimizeMover)

it says "interface_cutoff_distance: Residues farther away from the interface than this cutoff will not be designed or minimized."

However, what is "the interface"? Is it:

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Does it make sense to perform Docking on a complex?

Category: 
Design

I am trying to design an orthogonal ligand/receptor system. I've inherited the script below as a starting point but I'm wondering what exactly the Docking mover would be doing. My PDB structure is a ligand that is already bound to the binding domains on the receptor. Does it still make sense to perform a docking step in this scenario?

My script:

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get an increased energy after energy minimization when using different score functions for repacking and energy minimization

Category: 
Design

Hi, 

I am a new user of rosetta. Now I meet some problem that I cannot solve. I am wondering whether you could please help me. I would much appreciated. 

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MotifGraft error: "Residue connection id changed when creating a new residue at seqpos"

Category: 
Design

Hello everyone,

I am trying to use MotifGraft mover to graft an epitope to a scaffold protein (actually there is a structure library, parsed with -l list).

The xml script is attached.

My command line is as follow (I am first trying a very loose boundary conditions, I'm aware about the higher RMSD/atom_clash values):

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ROSETTA design affinity optimization

Category: 
Design

Hello

I'm trying to to use rosetta design (http://rosettadesign.med.unc.edu) to increase binding affinity between 2 proteins in 1 pdb file. 

I want 2 residue ranges to be mutated in chain B but all other residues to remain the same. Therefore I have used this resfile:

NATRO

start
71 - 88 B ALLAAxc EX1
50 - 56 B ALLAAxc EX1
 

However, the server mutates residues in both chains. How do I force it to only mutate chain B?

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