/RNA-ERGY

This program provides tools for creating and training an objective function on known 3D RNA structures, evaluating predicted RNA structures, and generating scoring profiles to optimize the 3D structure of RNA molecules

Primary LanguagePython

RNA-ERGY

This program contains various scripts for creating and training an objective function on a dataset of known (experimentally determined) 3D RNA structures. The objective function estimates the Gibbs free energy of a given structure, which can be used to evaluate and compare the stability of predicted RNA structures. In addition, this program includes scripts for generating scoring profiles, which plot the estimated Gibbs free energy as a function of interatomic distances. With these tools, you can optimize the 3D structure of RNA molecules and gain insights into their stability and function

Installation

  1. Clone the repository from GitHub:
git clone https://github.com/h-escoffier/RNA-ERGY
  1. Navigate to the directory where the repository was cloned:
cd RNA-ERGY
  1. Install the necessary dependencies for the program using pip:
pip install -r requirements.txt

Usage

training.py

This script builds and trains an objective function using a dataset of 3D RNA structures that have been determined experimentally.

python3 trainig.py path_to_pdb_folder

plot.py

This script generates scoring profiles, which plot the estimated Gibbs free energy as a function of interatomic distances.

python3 plot.py 
or 
python3 plot.py path_to_energy_folder

scoring.py

This script uses the objective function to evaluate the accuracy of predicted structures from an RNA pdb file.

python3 scoring.py path_to_pdb_file
or 
python3 scoring.py path_to_pdb_file path_to_energy_folder

Arguments

The following arguments can be used with this script:

  • path_to_pdb_folder: Provide the path to a file containing one or more RNA files in .pdb format. You can use the 'PdB_Folder' file provided in the code as an example.
  • path_to_energy_folder: Provide the path to a folder that holds the scoring values for each base pair, which are generated by the training.py script. The default name of this folder is 'Energy'.
  • path_to_pdb_folder: Provide the path to a file containing one or more RNA files in .pdb format. You can use the 'PdB_Folder' file provided in the code as an example.
  • path_to_pdb_file: Provide the path to a the pdb file for an RNA molecule.
  • -h, --help: Display a list of available arguments and their descriptions

Project developed as an examination for the GENIOMHE master's degree.