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Building loop extensions in a membrane protein with Remodel

Submitted by benhardy on Tue, 2020-06-02 08:21
Category: 
Design
Scoring
Loop Modeling
Membrane

Hi All,

I was wondering whether Remodel is currently compatible with the RosettaMP framework? I have a designed membrane protein and I'm trying to alter the sequence of water-exposed loops, which involves a few insertions. I'm using Remodel to do this but haven't been able to run it using the franklin2019 scorefunction.

Here are the flags that I'm using:

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Rosetta 3 - Applications

mp_transform optimize with franklin2019 scoring

Submitted by benhardy on Thu, 2020-05-28 08:35
Category: 
Design
Scoring
Enzyme Design
Membrane

Hi All,

I am running some flexible backbone design on a transmembrane four-helix bundle heme protein via RosettaScripts. I'm finding that the membrane residue is moving a lot during design, and I have to optimize the embedding with mp_transform post-design to reposition the mem residue. I have a few questions about this:

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Rosetta 3 - Applications

RosettaAntibodyDesign: How can I run the protocol without allowing design?

Submitted by brspurri on Tue, 2020-05-26 08:12
Category: 
Structure prediction
Docking
Design

Hi there,

I am trying to use RosettaAntibodyDesigner without allowing any design elements of the protocol to occur. I understand 100% that this would remove the intended purpose and use cases of RAbD, however, I am trying to piecemeal a side-by-side comparison of a designed mAb (which works reat through this protocol) and a non-designed mAb. 

However, I would like to ensure that both my simulations are executred identially otherwise. (ie., loop flexibility in docking, etc).

Is there any way to runn RAbD while FIXing all the CDRs?

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Rosetta 3 - Applications

Changing rosetta scoring to favour less hydrophobic areas

Submitted by daniloboskovic on Thu, 2020-05-21 03:03
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 3 - Applications

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

Submitted by cm21 on Wed, 2020-05-20 08:55
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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Rosetta 3 - Applications

Side-chain grafting at the fixed protein and position

Submitted by Kazu on Wed, 2020-05-20 08:49
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

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Rosetta 3 - Applications

Side-chain grafting in fixed scaffold

Submitted by Kazu on Wed, 2020-05-20 08:45
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

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Rosetta 3 - General

Multistate design issues with -run:msd_job_dist option and MSDMover

Submitted by elaine.thai on Wed, 2020-05-13 18:07
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:

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Rosetta 3 - Applications

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