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Help - Protein-Protein interface design

Submitted by Dinesh Kumar on Thu, 2021-01-28 00:47
Category: 
Design

Hello everyone!!

I am trying to work on the protein-protein interface design using rosetta scripts.  I am new to running rosetta scripts. So, I kindly need help on that. 

I ran the configure file given in the first step which threw me an error of Nobsub in path. I tried installing bsub and adding paths to the bash file but still wasn't able to proceed further. 

Kindly help me out if there are any mistakes or details i may have missed in setting up the run.

Thanks in advance

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Rosetta 3 - General

CoupledMoves not altering backbone coordinates?

Submitted by amorin on Wed, 2021-01-20 11:38
Category: 
Design

HI All,

I'm beginning to play around with CoupledMoves for flexible backbone design and I am unable to get it to alter the protein backbone coniguration.

When I run the tutorial here (https://github.com/Kortemme-Lab/coupled_moves-tutorial) it works. But when I try and apply that (or similar) command to another protein it will deisgn the sequence, but all the output pdbs have no coordinate changes. 

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Rosetta 3 - Applications

De novo backbone trace from fragments

Submitted by Victor Tobiasson on Tue, 2020-12-22 06:34
Category: 
Structure prediction
Design
Loop Modeling

Dear Rosetta experts,

I have been using rosetta mainly for refinement and iterative local rebuilding into cryo-em densities at reolustions of ~3-3.5 Angstrom. I am wondering how (or if it is possible) to combine and complete a set of backbone fragments predicted by external software into a single backbone trace using rosetta. To make matters somewhat more complicated I would need to do this without any sequence information using only polyA fragments.

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Rosetta 3 - General

RosettaScripts filter BuriedUnsatHbonds2 missing still

Submitted by zdaw on Fri, 2020-12-11 12:39
Category: 
Design

Hello, 

Can the BuriedUnsatHbonds2 filter be pushed to release? It gets called in a rosetta scripts xml included in the supplementary materials for this paper (published in 2017): DOI: 10.1126/science.aan0693

 

Thanks!

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Rosetta 3 - Applications

symmetric design w/ hbnet and unsatisfied_buried_penalty score terms

Submitted by saz on Tue, 2020-12-08 11:37
Category: 
Design

Hi All,

I am working on designing some symmetric structures and am currently using REF2015 + hbnet. In addition, I want to add the buried_unsatisfied_penalty. When I add this term to the score function, it works and can score 'non-symmetrized' structures just fine. However, when I try to score a structure that has been 'symmetrized' I get the following error: 

File: /home/benchmark/rosetta/source/src/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraph.cc:637

[ ERROR ] UtilityExitException

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PyRosetta - Scripts

Can I believe the antibody design result?

Submitted by Sunyp_IM on Mon, 2020-11-30 03:29
Category: 
Design

I am trying to do antibody design with the  RosettaAntibodyDesign, but some of my colleagues told me that they fell to obtain successful designers with the  RosettaAntibodyDesign (RAbD). They ran the RosettaAntibodyDesign on the crystal structure of an ab-ag complex with a dG_seperate of about -20 REU, and got some designers with dG_seperate of about -40 REU. However, they did experiments including ELISA and SPR and found that these antibody designers did not bind to the antigen at all!

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Rosetta 3 - Applications

How to use MHC Epitope energy (mhc_epitope) to deimmunize a protein structure?

Submitted by Sunyp_IM on Sun, 2020-11-08 08:07
Category: 
Design

Dear all,

The MHC Epitope energy (mhc_epitope) alogrithm  (https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/MHCEpitopeEnergy) is for deimmunization of epitopes. However I cannot understand how to use it. 

I used the pdb file 2b3p.pdb and the score controlling script in the introduction webpage as the inputs and run the following command:

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Rosetta 3 - Applications

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