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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).

Post Situation: 

mpi_MSD for antibody design

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

Post Situation: 

Segfault error while running MR Rosetta in Phenix

Category: 
Phenix / MR Rosetta

Hello,

In the middle of my MR Rosetta run I got a "Failed to run REBUILD" error. I am at a completely loss for how to solve this problem. Error logs are attached.

I am running rosetta_src_2021.16.61629_bundle on Phenix 1.19.2-4158. I did notice the Phenix instructions for installing Rosetta mention using Rosetta version 3.10 or later, is that the reason for the fail?

Thank you!

Post Situation: 

Global ligand docking with Rosetta script and PyRosetta

Category: 
Docking

Hi all,

Is it possible to perform global ligand docking with Rosetta script not PyRosetta?

I found the tutorial for global ligand docking in PyRosetta. ( https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.01-Ligand-Docking-XMLObjects.ipynb )

But, I could not find any explicit example for global ligand docking with only Rosetta script.

Thank you,

Post Situation: 

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