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Changing rosetta scoring to favour less hydrophobic areas

Category: 
Design

Dear contributors,

I'd like to change the rosetta scoring function in remodel to favour models that have less hydrophobic area. Main reason is low computing power for the task at hand.

Changing fa_sol is definitely the option? Should i change the lk_ball_wtd as well?

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Rosetta Antibody Design: Error with foldtree: problem with the fold_tree:biggest_label != num_jump 2 1

Category: 
Docking
Design

Hi all,

I'm attempting to use Rosetta Antibody Design (RAbD) v2019.35.60890 to design antibodies for a protein whose structure is a trimer.
BACKGROUND: I can successfully run the RAbD protocol on the ful trimer structure from the PDB (6VXX) with the following command:

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Side-chain grafting at the fixed protein and position

Category: 
Design

Hello folks,

I’m trying to transfer a epitope to the protein of my interest at the designated position which is composed of alphahelix. 

Previously, several antibodies have been shown to recognize the alphahelical conformation such as PDB:3LRH. 

So I wonder if I can transfer the epitope to the designated position while keeping its ability that is recognized by the corresponding antibody. That is something like

Post Situation: 

Side-chain grafting in fixed scaffold

Category: 
Design

Hello folks,

I’m trying to transfer a epitope to the protein of my interest at the designated position which is composed of alphahelix. 

Previously, several antibodies have been shown to recognize the alphahelical conformation such as PDB:3LRH. 

So I wonder if I can transfer the epitope to the designated position while keeping its ability that is recognized by the corresponding antibody. That is something like

Post Situation: 

Multistate design issues with -run:msd_job_dist option and MSDMover

Category: 
Design

Hi there,

I'm trying to perform multistate design using Rosetta 3.11 to improve antibody binding to five slightly different epitopes. I've been following the tutorial provided by the Meiler Lab and I've been able to successfully prepare my input files, but I'm having issues running the design.

First, when I tried to run the design using the attached .options and .xml files, but I got the following error:

Post Situation: 

Error with filter in rosseta_scripts

Category: 
Design

Hi 

i am working inthe design of peptides using the genkic mover. I am trying to implement a filter with "PeptideInternalHbondsFilter" to remove unwanted structures. When i run the rosetta_scripts  command this is the output.

From line 42:
Error: Element 'PeptideInternalHbondsFilter': This element is not expected.

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BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?

Category: 
Design

I triple checked my protein PDB file, and i used the script to get a blueprint file. It has no chain definitions and is perfectly in order. Error happens when a succesful closure is made. If the closure is not successful, it continues. Also, if i set G or POLAR instead of ALLA, it works.

Post Situation: 

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