RosettaCommons - PyRosetta - Applications

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Scoring function for disordered peptide ddG calculations?

austin.weigle.usda — Tue, 28 May 2024 21:52:28 +0000

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

I know from my experience that there is a function specific for membrane proteins, and that there is something like a default scoring function in REF2015 (https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/score-types). Is there any documentation to point out specific scoring functions for different applications, including disordered proteins or peptides?

Thanks,

Austin Weigle

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Demo scripts for proteinmpnn in pyrosetta

lwhitm1 — Thu, 09 Nov 2023 01:57:57 +0000

Are there currently any demo scripts/usage examples for using proteinmpnn in pyrosetta? I've found the module documentation here:https://graylab.jhu.edu/PyRosetta.documentation/index.html

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NMR NOE based structure prediction

Pooja — Mon, 25 Sep 2023 06:39:29 +0000

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

franz72 — Sun, 17 Sep 2023 21:08:14 +0000

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

!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init('-ex1 -ex2 -use_input_sc -no_optH false -flip_HNQ -nstruct 1')
from pyrosetta import *
from pyrosetta.teaching import *
#input pdb file
pose = pose_from_pdb('unrelaxed_97.pdb')
#shorten name
fr = pyrosetta.rosetta.protocols.relax.FastRelax()
#get ref2015 scoring function
fr.set_scorefxn(get_score_function())
#flags from benchmark study Yin et al., 2022
fr.constrain_relax_to_start_coords(True)
fr.coord_constrain_sidechains(True)
fr.ramp_down_constraints(False)
#run FastRelax
fr.apply(pose)
#download relaxed structure
pose.dump_pdb('relaxed_97.pdb')

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InterfaceAnalyzerMover with more than two chains

franz72 — Fri, 04 Aug 2023 15:33:16 +0000

Hi,

I hope this message finds you well. I would like to use the InterfaceAnalyzerMover to determine the seperated interface energy difference between three or four chains. I noticed in the metadata page for InterfaceAnalyzer there are two flags to accomplish this (link). However, I could not find these flags in the PyRosetta 4.0 documentation describing InterfaceAnalyzerMover, and I am not sure how you would use these flags in Python (link).

These are the flags I am looking for (link):

"-interface (string) - Multichain option. Which chains define the interface? example -interface LH_A to get the interface between chain groups LH and A. Works for sub interfaces such as L_H by ignoring any chains not specified in calculations. Not tested thoroughly beyond three chains.

-fixedchains (string) - Multichain option. Which chains are in the two groups to define the interface? example: -fixedchains A B to keep chains A and B together, and C separate, out of a pose that contains A, B, and C. Note a space between A and B. Analogous to -interface option. Includes all chains of the pose. Not tested thoroughly beyond three chains."

On a separate note, I noticed ref2015 is the default scoring function. Is this still the preferred scoring function for determining binding affinity? If not, what would be the best way to change it?

Also, I noticed there is a set_pack_rounds() function, and the default is one round of packing. How can I know if this is enough?

I have attached the code I am running, as it is now below, in case that is helpful. Please let me know your thoughts when you have time.

Thank you,

Franz

#Get PDB file
pose = pose_from_pdb("name.pdb")

#Run InterfaceAnalyzerMover
ia = pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover()
ia.set_pack_input(True)
ia.set_pack_separated(True)
ia.set_use_tracer(True)
ia.apply(pose)

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Scoring

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Ab initio peptide design to use as ligands in docking

archaeopteryx — Tue, 27 Jun 2023 18:09:04 +0000

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)

# Relaxa a pose
relax = pyrosetta.rosetta.protocols.relax.FastRelax()
relax.set_scorefxn(scorefxn)
relax.apply(pose)

# Calcula e imprime o score após o relaxation
score_after_relax = scorefxn(pose)
print('Sscore pre relax:', score_before_relax)
print('Score pos relax:', score_after_relax)

pose.dump_pdb('relaxedpeptide.pdb')

I don't know why but I can't insert them in DockThor platform, it shows an error when I try. When I open the .pdb pose in a text editor, there's no CONECT section as other .pdb files from cristalized peptides, I think maybe that can be the reason.

Is there some protocol to create small peptides (9~13 residues) for use in docking?

thanks

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ideal A-form RNA Helix

tspich — Wed, 17 May 2023 10:01:25 +0000

The tutorial (https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb) claims that using:

assembler = core.import_pose.RNA_HelixAssembler()
helix_pose = assembler.build_init_pose('ggggggg','ccccccc')

should generate an ideal A-form RNA helix. However, the longest the sequence the closer the base pairs are coming together and a non relasitc helix is produced (see rna.png).

Am I missing something to get an ideal A-form RNA helix?

Attachment	Size
rna.png	119.76 KB

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Nucleic Acids

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How to use pyrosetta to generate decoys of RNA with different RMSDs (e.g. 1Å, 5Å, 10Å).

Alice123 — Sat, 18 Feb 2023 02:24:38 +0000

I am a beginner in pyroseta and now need to use pyrosetta to generate decoys of RNA with different RMSDs (e.g. 1Å, 5Å, 10Å), I checked the manual but it is still not clear, can you give me some guidance, thank you!

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Rosettasurface in Pyrosetta 4

Oaham — Tue, 23 Nov 2021 07:35:40 +0000

Greetings,

I would like to dock a small protein on a metal surface. It may be similar simulations which has done by Jeff Gray's group. But I found the code in surface_docking was written for pyrosetta 2 based on python 2.x . I have tried to transform the script to python3.. However, unknown errors appeared all the time.

Can anyone tell me how to use these code in Pyrosetta4 (python3) or provide any detailed tutorial for surface_docking in Pyrosetta4?

Thanks very much!

Hao

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Docking

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