Background

Understanding Communication Networks in Molecular Complexes

compass is an advanced computational tool that analyzes the communication networks between protein-protein and protein-nucleic acid complexes. It leverages molecular dynamics (MD) simulation data to extract essential inter-residue properties, including dynamical correlations, interactions, and distances. For a comprehensive methodological introduction, please refer to the following paper.

Installation

The installation of compass is straightforward. Just type the following commands in your terminal (assuming you've got Anaconda or Miniconda up and running):

   git clone https://github.com/yasamankarami/compass.git
   cd compass
   conda env create -f environment.yml
   conda activate compass  

Basic usage

As a command-line tool, compass requires only the path to a well-structured configuration file (refer to the documentation for instructions on preparing it). Once installed, you can run it using the following command:

   compass path-to-config-file.cfg

Documentation

For comprehensive documentation and tutorials, visit the wiki.

Contributing

If you are interested in contributing to the project, please review the guidelines in the CONTRIBUTING.rst file.

License

This project is licensed under the BSD 3-Clause License. For more details, check the LICENSE file.

Citation

If you use compass in your research, please let us knoow by citing the following paper::

Bheemireddy S, González Alemán R, Bignon E, Karami Y. Communication pathway analysis within protein-nucleic acid complexes. bioRxiv. 2025:2025-02.