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How to choose designed antibody

Category: 
Design

Dear all,

I am trying to use Rosetta dock and antibody design modules to design antibody in order to improve the affinity of the antibody to the antigen.  Firstly I docked the antibody to the antigen. In this step I got 500 and antibody-antigen complex models and selected top 10 models based on the lowest I_sc energy. Then I ran AntibodyDesign using a command like the follow for each of the 10 complex models:

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Coupled Moves crash with Membrane Protein - residue_edge is undefined for root vertex

Category: 
Design
Membrane

Hi All,

I came across the Coupled Moves protocol recently and it sounds like an interesting alternative to FastDesign that I've been predominantly using. I tried to implement the CoupledMoves Mover within my RosettaScripts design script, however, I keep coming across the following error:

ERROR: FoldTree:: residue_edge is undefined for root vertex
ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 2317
[0m[0mprotocols.rosetta_scripts.ParsedProtocol: [0m[31m[1m[ ERROR ][0m Exception while processing procotol: 

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Difference between interface_delta_X and dG_separated?

Category: 
Design

Hi, everyone!

I am using RosettaLigand design protocol to design some mutants, in order to improve binding affinity to a small molecule. When I was using InterfaceAnalyzer, there were 2 values representing binding affinity, interface_delta_X and dG_separated. I want to know the difference between these 2 values and which one I can use during the filter process.

Any suggestion will be appreciated!

Nicole

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Building loop extensions in a membrane protein with Remodel

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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mp_transform optimize with franklin2019 scoring

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

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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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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