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Design

Domain insertion with Non-CAA

Category: 
Design
Loop Modeling

Hi all,

I am trying to insert a long fragment (GFPStrand) into another protein (4e1s) using Remodel. I've delete the residues that were originally in 4e1s but left a few at the end as an anchor for the domain insertion. Remodel throws an error about insertion indices being 0 if I don't leave them to anchor it. Remodel accepts the domain insertion and starts on the loop closure. It also appears to close the loop, but then throws this error with trace: 

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Altering substrate specificity

Category: 
Design
Scoring
Enzyme Design
Small Molecules
Chemically Modified Residues

Hi all,

I'm presently working on a project to modify the substrate specificity of a DNA polymerase for non-natural nucleic acids.

I've currently been using the GreedyOptMutationMover with a ddg filter (jump across the substrate) for a 10Å shell around the active site and identified several single point mutations that have been experimentally validated to improve activity.

However, one of the problems with greedyopt is that it does not appear to screen every possible position or single point mutation within the designable region.

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Error using FilterScan with rosettascripts

Category: 
Design

Hi,

I'm trying to perform a residue scanning of an interface in order to identify potential mutations that can improve affinity.  I tried using the FilterScan filter:

<ROSETTASCRIPTS>

    <SCOREFXNS>
        <t14 weights="talaris2014"/>
    </SCOREFXNS>
    

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Design with limited number of aminoacids at given position

Category: 
Design
Constraints

Hi!

What is the easiest way to allow only a single residue type (e.g. Trp) at a given position during the design?

I use FastDesign Mover with symmetry. I thought about ReadResfile and PIKAA command, but perhaps it could be done directly from the Rosetta Script? Via task_operations=... ?

Best wishes,

Staszek

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Ddg_monomer: implementing disulfides

Category: 
Design

I've been using the ddg_monomer application with high resolution protocol flags and the alternative mutation file format (to obtain more than one mutation) on the constant domain of a TCR (alpha and beta chain).

 

I'm interested in 3 ddg values:

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Symmetric design with PyRosetta

Category: 
Design

Hello,

 

Is it possible to do symmetric design with PyRosetta4 ?

 

I try to pass a symmetry flag to the command line and run pack_rotamers but I get a warning saying that I try to

use a symmetric score function on a non symmetric protocol or something like that.

 

In previous Rosetta versions, there was a symmetric_pack_rotamers, but this method disappeared and there is some symmetry code in

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Should FastRelax be commented out in Calculate_protein_protein_ddg demo?

Category: 
Design

Here's the source code of mutation_script.xml, part of the demo calculate_protein_protein_ddg included in Rosetta (see https://www.rosettacommons.org/demos/latest/public/calculate_protein_protein_ddg/README). I deleted the comments to make it shorter:

 

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RosettaMatch outputs

Category: 
Design
Enzyme Design

I've been running several rounds of RosettaMatch lately and I'd like them to go faster. I'm pretty sure writing matches is the part slowing it down. Is there anyway to limit the number of matches it outputs? For example, for the same matched sequence (say H133H135H432), I get anywhere from 50-400 cloudPDB files. I don't want more than the first one or two, because the rest are almost always just different ligand positions and I'll end up running EnzDesign anyways. I'm using these flags:

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