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

Submitted by CordycepsLin on Sun, 2022-02-06 19:09
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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Rosetta 3 - Applications

Can anybody suggests some flags to run Rifdock?

Submitted by Hyunmi Song on Sun, 2022-01-23 16:45
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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Rosetta 3 - Applications

Scripts accompanying Hossenzadeh et al, 2001

Submitted by Ken on Wed, 2022-01-19 07:38
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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PyRosetta - Scripts

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

Submitted by tlopes on Wed, 2022-01-05 18:19
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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Rosetta 3 - General

mpi_MSD for antibody design

Submitted by hanzhiz on Thu, 2021-12-16 09:32
Category: 
Design

Hello All,

 I have a few questions on a paper from Kuhlman's group "Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface"

https://www.nature.com/articles/nbt.2797

 

In the method section, there is an MSD protocol for CL-CH1 interface. And following is the fitness file:

#-12 is the energy cap, determined empirically as the rough value of redocked binding energy for the worst mutations

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Rosetta 3 - General

How to apply cartesian_ddg to multi-metric enzyme?

Submitted by Wang Zhe on Wed, 2021-12-08 10:07
Category: 
Design

Hello,

 I would like to compare stability of the wild-type and mutated proteins(multi-metric enzyme) using cartesian_ddg. But I am confused about which one is suitable structure input. And I have two ideas now:

  1. Relax the whole enzyme, calculate each chains' ddg, and finally average the numbers.
  2. Split the enzyme complex into subunit monomers, calculate each monomers' ddg,  and finally average the numbers.

 

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Rosetta 3 - Applications

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