https://github.com/nrbennet/dl_binder_design's ProteinMPNN-FastRelax modification to screening of AF models of binding affinity #205
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sungyounjoo
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PyRosetta
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Hello,
I'm a beginner with PyRosetta, and I’ve been working on peptide binder design. I would like to use the "ddg_filter & ddg_hydrophobic_filter" from this GitHub repository. There is a "RosettaFastRelaxUtil.xml" file provided, and I have adapted the following Python script, which seems to work:
RosettaFastRelaxUtil.txt
import os
import glob
import gc # For memory management
from pyrosetta import init, pose_from_pdb
from pyrosetta.rosetta.protocols.rosetta_scripts import XmlObjects
from pyrosetta.rosetta.core.scoring import ScoreFunctionFactory
from pyrosetta.rosetta.protocols.analysis import InterfaceAnalyzerMover
Initialize PyRosetta with the appropriate options
init("-ex1 -ex2aro -corrections::beta_nov16 -mute all")
Load the RosettaScripts XML file
xml_file = "RosettaFastRelaxUtil_original.xml"
xml_objects = XmlObjects.create_from_file(xml_file)
Get the FastRelax mover and ddG filters from XML
fast_relax = xml_objects.get_mover("FastRelax")
ddg_filter = xml_objects.get_filter("ddg")
ddg_hydrophobic_filter = xml_objects.get_filter("ddg_hydrophobic")
Load AlphaFold models (assuming in PDB format)
af_model_dir = "./test"
af_models = glob.glob(os.path.join(af_model_dir, "*.pdb"))
Iterate over each model, apply FastRelax, and calculate ddG
for model in af_models:
print(f"Processing {model}")
print("Processing completed.")
What I would like to ask is regarding the validity of this script: does it provide similar results to the original ddG filter from the GitHub repository? (As a beginner, I couldn’t fully follow the details of the original scripts.)
Additionally, I would appreciate your opinion on whether using this script for ddG filtering is appropriate for research purposes.
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