Awesome

parametric_barrels

Description

This repo includes utility scripts to generate parametrically guided beta barrel protein backbone structures.

Reference

Kim, D.E. et al. Parametrically guided design of soluble beta barrels and transmembrane nanopores using deep learning. 2024

Installation

You can clone this repo into a preferred destination directory by going to that directory and then running:

git clone https://github.com/davidekim/parametric_barrels.git

Usage

barrels.py is the main script that generates parameter defined barrel cylinders used as input for RF partial diffusion and RFJoint2 inpainting beta barrel structure refinement.

python ./barrels.py --n 6 --S 10 --nres 10

check_barrels.py is a utility script that evaluates beta barrel outputs from RF partial diffusion and RFJoint2 inpainting to determine the extent of beta barrel formation.

python ./check_barrels.py <pdblist> <cylinders dir>

Dependencies

PyRosetta https://www.pyrosetta.org

BBQ https://biocomp.chem.uw.edu.pl/tools/bbq

silent_tools https://github.com/bcov77/silent_tools

Support

Contact David Kim (dekim@uw.edu) for any questions.