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Design

Model two domain protein

Category: 
Design

Hi,

I want to model a protein that has two domains. I have two separate domains modeled using Rosetta. I want to merge these two domains based on the cst file that gives inter domain distance constraints.

What are some of the best ways to model it? These domains are  asymmetric. Can I use RosettaCM to do the modeling? Or should it be more like fold and dock?

 

Post Situation: 

optimisation of a protein-protein interface

Category: 
Design
Scoring
Symmetry

Dear Rosetta users,

I have a symmetrical homo-dimeric structure for which I would like to select a single point mutation that will increase the affinity between the monomers. I thought about design&relax protocol, in which one position is designed while the remaining ones are only allowed to repack. Such a protocol would be used to scan all the interface positions.

My questions is how to set up this in Rosetta Scripts? Perhaps there are easier/better ways to do this?

Thanks for help! Staszek

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Fast relax not working

Category: 
Design

Hi I have not used Rosetta for a while.  i wanted to relax my receptor for enzyme design and i kept on having the message

Evaluation Creator active ... 

protocols.relax.FastRelax: WARNING: Pose has no residues. Doing a FastRelax would be pointless. Skipping.

protocols.jd2.JobDistributor: S_0001 reported success in 0 seconds

protocols.jd2.JobDistributor: no more batches to process... 

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs att

here is my flag file

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Error using InterfaceHoles filter

Category: 
Design

Hi,
I'm trying to use the InterfaceHoles filter and get the following error:

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER holes=======================
core.scoring.packing.compute_holes_score: compute_holes_surfs try: 1
sh: 1: alpha20_surf: not found

Any idea where alpha20_surf needs to be (or if it needs to be compiled?)

 

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cxx11 error with antibody modelling

Category: 
Structure prediction
Design

Dear all,

I built the last release 2017.08 recently. I have not encountered any error during the build. Here is the command I ran:

./scons.py -j8 mode=release bin extras=cxx11 extras=mpi

I have gcc version 5.4.0 so according to build tutorial this should new enough to have C++11 support. 

But when I am running antibody.linuxrelease as according to the protocol on

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Looking for collaboration.

Category: 
Design

​Dear Rosetta Community,

 
I am searching for labs in the UK that uses rosetta to design proteins for collaboration. Is there a list of all labs that either develop or use rosetta?
 
Why the UK? becuse the funding I will bring will be from a UK based institute.
 
Just a list, or where I can find one, will be helpful enough.
 
Thank you.
Post Situation: 

KeyError: 'subject-id' in antibody modelling

Category: 
Structure prediction
Design

Dear all,

I have recently started learning Rosetta. Now I am working on antibody modelling. I have prepared my inputs, have blast and Pro-Fit working.  When I am running the antibody.py with the default preprocessing options

Post Situation: 

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