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pro's Introduction

PRO is a Python application for the fast protein structure optimization. It is rapid alternative to protein structure optimization with constrained alpha carbons. During the PRO method, the entire structure is not optimized at once but individual residues are optimized sequentially. The main advantage of such approach is its linear time complexity with respect to the number of atoms, where the optimization time is usually about 0.14 second per atom.

How to install

To run PRO optimization you will need to have Python 3.11 and package manager Conda installed.

Then, clone project and install the project dependencies by running:

$ git clone https://github.com/sb-ncbr/pro
$ conda install scipy=1.11.3 biopython=1.81 openbabel=3.1.1 xtb=6.6.1

How to run

Run the PRO optimization by running the following command inside github repository:

(venv) $ python3.11 pro.py --PDB_file <path_to_file> --data_dir <directory_to_store_data>

License

MIT

pro's People

Contributors

dargen3 avatar

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