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Structure prediction

VH-VL Orientation in antibody

Category: 
Structure prediction

 

How to determine the VH-VL orientation angle in rosetta. i came across this manuscript "Improved prediction of antibody VL–VH orientation" by Protein Eng Des Sel. 2016 Oct; 29(10): 409–418. Here there is description of MT protocol. Whether the script is provided in the rosetta 3.1 version. Or is there any other alternative in rosetta to calculate the VH-VL orientation (LHOC) angle of antibody in rosetta.

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Membrane ab-initio modelling of a beta-strand

Category: 
Structure prediction

Hello everyone!

We're trying to model a membrane peptide of ~50 aminoacids which likely assumes beta-strand conformation in the membrane. Can we do this with the current Ab Initio membrane implementation of Rosetta? I know that we should use Octopus to generate a span file, but I'm left with the impression that it's designed for alpha helical proteins and that Rosetta in general is biased toward generation of alpha helices. Is there a way to enforce some beta-sheet restrictions during the ab initio folding process?

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LHOC script problem in Rosetta Antibody

Category: 
Structure prediction

Hi all,

I'm getting a problem running the LHOC angle script in the antibody modeling protocol. To reproduce:

python -m pdb ../rosetta/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/plot_LHOC.py -h3_fasc H3_modeling_scores.fasc -graft_dir grafting -output_dir vhvl

I have uploaded the H3_modeling_scores.fasc file and the contents of the grafting directory. Here is the error message:

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Rosetta params for taxol

Category: 
Structure prediction

I want to use RosettaCM for density guided homology modeling. My structure contains taxol and other ligands: GTP and GDP, but my /rosetta/main/database/scoring/score_functions/facts contains params files for just GTP and GDP but not taxol. I atatched my taxol.pdb file for reference. 

Thanks in advance. 

 

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Does Snugdock remodeling of H3 loops include the kink constraint as in RosettaAntibody?

Category: 
Structure prediction
Docking

I am docking an antibody that has 20 residues in the H3 loop.  I realize that this is a very challenging case.  From the 2017 paper by Weitzner and Gray, I understand the importance of a kink constraint in H3 loop modeling.  I want to know if the H3 loop remodeling that occurs during snugdock includes the kink constraint.  If not, I am concerned that the kink will be lost during remodeling, especially for this long loop.

 

 

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Error with simple_cycpep_predict protocol while using a native pdb file

Category: 
Structure prediction

Hello Rosetta devs,

 

I'm not sure that this is the right place to post a bug. If not, please let me know where to post.

 

I compiled both Rosetta 3.10 (and then 2019.07 release), and faced the following error when trying to predict cyclic peptides with terminal disulfide bonds using the simple_cycpep_predict protocol.

To be more specific, my peptide has a non-terminal CYS residue at the C-term, and I was using the

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Abinitio the Broker protocol

Category: 
Structure prediction

Hello everyone,

I am reading about the Abinitio protocol to see how I can include a checkpoint file in the Abinitio flags, but i could not find any information on how to input a checkpoint file. so this is my question:

  • can I input a checkpoint file into Abinitio? if i can what is the flag     -in:file:  ?

 

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