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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

Segfault error while running MR Rosetta in Phenix

Submitted by memilton on Thu, 2021-12-16 09:09
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!

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Rosetta 3 - Applications

Global ligand docking with Rosetta script and PyRosetta

Submitted by tisozaki on Tue, 2021-12-14 17:16
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,

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Rosetta 3 - General

compiler option not found

Submitted by stranges on Wed, 2021-12-08 10:28
Category: 
Compilation

Hi all,

I recently had to update my OSX command line tools and in doing so went from clang 12.0 to 13.0

I'm trying to compile Rosetta build 2021.16.61629 and am running into an issue. I was previously able to compile fine with clang v12.0.

As far as I can tell there seems to be an issue with the -rpath option, but that doesn't make much  sense. See the fail point and error messages below.

Not sure if this is a zlib issue given the fail point. As far as I can tell I have zlib installed properly. 

 

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Rosetta 3 - Build/Install

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

Relaxed proteins show higher clash score in molprobity results.

Submitted by Wang Zhe on Fri, 2021-12-03 04:32
Category: 
Structure prediction

Hi everyone,

I am tring to refine the predicted structure from alphafold and SWISS-MODEL database. Since the protocol I followed said I need to eliminate the steric clash and do refinement in predicted structure first (and then docking or some other analysis).

So I just relaxed protein in torsion space with constraints. And here is the code I used:

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Rosetta 3 - Applications

Question about running scallo

Submitted by danbo on Mon, 2021-11-29 23:25
Category: 
Scoring

 I am trying to run code on https://github.com/strauchlab/scaffold_design

but it occur an error :

basic.io.database: [ WARNING ] Unable to locate database file scoring/score_functions/aa_composition/%%aa_comp%%.comp
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'startingstub_0000_0008_0001'
Error: [ ERROR ] 

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Rosetta 3 - Applications

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