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PyRosetta

Scoring function for disordered peptide ddG calculations?

Category: 
PyRosetta

I am looking to do a ddG analysis on some peptide structures that I have developed through simulation. Previously, I have used pyrosetta for performing ddG analyses on membrane proteins. In that case, I was able to use the franklin_2019 weights as my scoring function.

Poking around, I have seen that there are a good number of weights files listed as:
/PATH/pyrosetta/lib/python3.9/site-packages/pyrosetta/database/scoring/weights/*.wts

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Unable to get non-commercial license to get username/password

Category: 
PyRosetta

Hi team,

As noted in the steps to get non commercial license, there is a license form people can fill up to register for username/password to use Pyrosetta. Seems the form is unable to find.

Thanks for assistance.

 

david

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Error about rifdocking step 15

Category: 
PyRosetta

I am still working on the Cao protocol. And I ran into another problem. When I ran step 15: Motif extraction. I ran the following command:
/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py -in:file:silent /home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/fd_output_splits/xaa.silent -ref_pdb /home/gaon/cao_protocol/protocol_test_E/input/output/rif_64_output_sca0.8_noKR.rif.gz_target_chainchanged.pdb -out_prefix mot_

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Installing pyrosetta for proteinmpnn use

Category: 
Design
PyRosetta

What is the best way to install PyRosetta for use with Protein MPNN? I am installing it for myself on an hpc cluster (redhat linux 8) and haven't found much documentation outside of that for the general PyRosetta install.


 

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NMR NOE based structure prediction

Category: 
PyRosetta

Based on the NMR NOE data, I want to use PyRosetta for the structure prediction of my peptides having unnatural amino acids. I went through the manual but couldn't find much information for structure prediction based on NMR data. It would be of great help if you cite protocols, scripts or literature used to determine the structure using NMR data in PyRosetta.

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Altered pLDDT scores after running FastRelax on AlphaFold Multimer output pdb files

Category: 
PyRosetta

Hello,

I hope this message finds you well. I noticed after running FastRelax on output pdb files from AlphaFold Multimer that the pLDDT scores encoded in the B-factor fields have been altered. Is there a way to avoid this and maintain the original pLDDT scores? I have attached the code I am running below. 

Thank you,

Franz

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How can I automate mutations with PyRosetta or other Rosetta software?

Category: 
PyRosetta

I need to create mutant peptides with Rosetta to use in Virtual Screening, the mutations need to be kinda ''random'' (not chosen directly by me) and, if possible, following an evolutionary bias (genetic algorithm). I'm really new at protein modelling and I have only used AlphaFold. Rosetta has many ways to use, and I'm kinda lost, should I use Rosetta Scripts or PyRosetta? Can I do this with both? I haven't found any tutorial that explains how to create mutant peptides following a genetic algorithm with rosetta :(  I don't know where to start.

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Ab initio peptide design to use as ligands in docking

Category: 
PyRosetta

I need to create peptides to use them as flexible ligands in docking (DockThor platform). I'm new at pyRosetta so I've only seen 1 tutorial until now. I'm using the following code

import pyrosetta
from pyrosetta import *
from pyrosetta.toolbox import *
init()

peptide_sequence = 'insert peptide sequence'
pose = pose_from_sequence(peptide_sequence)

scorefxn = get_fa_scorefxn()

# define variavel score before relax
score_before_relax = scorefxn(pose)

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