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The problem hasn't been solved
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).
I am running the protocol from here https://github.com/LPDI-EPFL/RosettaSurf/tree/main/scripts/interleukin_benchmark. The .xml script works fine however I keep getting the following error at the end:
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"
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
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?
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.