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application for affinity optimization

Category: 
Design

Hello

Which application is suited for increasing affinity between 2 proteins? I would like to specify ranges of residues to be mutated in only 1 of the proteins/chains, e.g. in a resfile. 

Essentially I want to do something like the opt-dG application in RAbD, but with ranges of residues a protein domain that is not an antibody. Can the opt-dG do this?

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Rosetta changing Atom Name in PDB ATOM record?

Category: 
Design

Looking at an output PDB file from Rosetta Design, I've noticed that some of the hydrogens have a numeric prefix attached to their atom name in the ATOM record of the PDB file (picture attached).

Does anybody know what this prefix indicates? According to the PDB website, that particular column (column 12) should just be empty, so it is surprising to see a numeric value there.

I believe this is also causing errors for me trying to use another software which analyzes PDB files, by not recognizing the atom name.

 

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nstruct vs. trials?

Category: 
Design

In RosettaScripts,

we can specific the number of target structures for the script to design via the

-jd2: ntrials X 

flag where X is the number.

However, in the GenericMonteCarlo mover used for iterative design, we can also specify the number of iterations via the "trials" argument.

My question is, are there any advantages/disadvantages to setting the nstruct number low but setting the trials number high, and vice versa? 

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Filter for fixed-bb design using RosettaScript?

Category: 
Design

Hello,

If I want to implement fix-bb design (or a slight variation of it) using RosettaScripts, what filter should I use?

Can I not use a filter if I'm just interested in generating a library of designs from multiple input structures with different backbone conformations?

Does it make sense to not use a filter, since (to my understanding) the packer will generally pick rotamers that have less energy than the original residue anyways and output a final score for the designed pose?

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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:

Post Situation: 

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