doi: https://doi.org/10.1101/2021.01.28.428710
This tool requires Python 3.7, as well as the latest versions of the following:
- ANDIS (standalone version)
- PyRosetta4
- Numpy
- Scipy
- Scikit-learn
- h5py
NOTE: This tool was tested on Ubuntu 20.04 LTS. Installation and requirements may vary on other operating systems.
After installing ANDIS, be sure to modify execution permissions with this
command: chmod +x ANDIS.
In main.py, please change the following variables found at the top of the file:
- Change QA_DIR to the absolute path of this tool's directory.
- Change ANDIS_PATH to the absolute path of your installed ANDIS directory.
You can install the required Python libraries using requirements.txt:
pip3 install -r requirements.txt
Remember to also download and install PyRosetta4 (http://www.pyrosetta.org/dow) before proceeding.
Example usage:
python main.py -i ./input_folder_name -o output_folder_name
The input folder must contain at least one protein model (PDB format) for this tool to work.
A sample output can be found in example/sample_output. It was generated using the following command:
python main.py -i ./example/T0953s2 -o ./example/sample_output
Developed by Mikhail Korovnik and Prof. Renzhi Cao at Pacific Lutheran University:
Please contact Renzhi Cao for any questions: caora@plu.edu (PI)