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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

connecting pdb files

Submitted by Hyun on Wed, 2021-11-17 22:32
Category: 
Design

Hi

I has been using RosettaRemodel -remodel:domainFusion:insert_segment_from_pdb for connecting pdb files such as connecting 1 helix pdb file and another 1 helix pdb file.

But it doesnt always work, is there another way to connecting two helices in different pdb file by loop? 

Im wondering what protocols can be used for connecting two pdb files with loop to generate 1 pdb file 

please help me 

Thanks

 

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Rosetta 3 - General

Help with file in article Kemp elimination catalysts by computational enzyme design

Submitted by Wenithor on Sat, 2021-10-09 07:23
Category: 
Design

Hello, I would like to ask for some help, regarding the article Kemp elimination catalysts by computational enzyme design, you would still have the transition state calculated by gauss, I need the output because I am trying to replicate the article, and I need the coordinates of the hydrogen being removed from the carbon in the transition state. Does anyone have these outputs?

Att. Thank you

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Rosetta 3 - General

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