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score against rmsd plot of designs

Category: 
Design

Hello, friends,

I was designing the "interface" (possible contacts) of a fusion protein using FastDesign. Since I was running the appliction on a laptop, so far only 200 designed models have been genrated.

I then went on to analyze the result anyway and tried to plot Score VS caRMSD (as shown in the attached file). Here are my questions:

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PackRotamersMover in another way

Category: 
Design

I want to design peptides, allowing redesign and side-chain packing, but no backbone changes. So far I'm using PackRotamersMover, but I would like to write my packer with fixbb instead to have more control.

 

My question basically is: why do the two following snippets of code not do the same? And what have I missed about PackRotamersMover in my version?

code 1:

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RAbD with N-term,Proline-like ncaa returns segmentation fault during CCDEndsGraftMover

Category: 
Design
Chemically Modified Residues
Fragment Generation

Recently I'm stumbling with rosetta RAbD application (version 2020.08.61146) in hope to modify an antibody whose antigen containing a non-canonical,N-term, and PRO-like aa ,namely the pyroglutamic acid in its epitope. 

I generated params file according tutorials in :https://new.rosettacommons.org/demos/latest/public/design_with_ncaa/README,with input mol file below.

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Can anybody suggests some flags to run Rifdock?

Category: 
Design

Hello

I've tried to design some miniproteins, by following up "Baker lab 2020, science" paper. 

I want to use Rifgen in Rifdock to make disembodied amino acid contact.

But I don't know what flags to start.

 

They said the initial job of rifgen will take a long time.

On the Rifdock tutorial page, they said "to contact somebody doing some similar jobs and use their flag as a starting point"

So can somebody share your flags?

 

 

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Scripts accompanying Hossenzadeh et al, 2001

Category: 
Design

Hi all,

I recently came across the paper titled "Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites" and wanted to try it out for myself. I downloaded the supplemental materials and tried to follow along the READMEs to test out Methods 1-4. But I am not able to actually get any of them to work even with the provided pdbs. Is anybody else having the same problem?

Here is what I have tried...

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Design strategy - One chain at a time OR two chains together?

Category: 
Design

Hello folks,

this is a conceptual question.

The protein I am working with has 2 domains (2 chains), and I would like to redesign part of the surface of each domain AND the interface between those domains.

I see two possibilities here (maybe there are more):

Option #1- Break the design into three smaller problems - i.e., design only chain A, then design only chain B, and finally, design the interface (5 residues + 7 residues  + 11 residues).

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