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netsci_paper

Data and calculations used for the Netsci paper:

Stokely A, Votapka L, Hock M, Teitgen A, McCammon JA, McCullough A, Amaro R, NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-fjrpp This content is a preprint and has not been peer-reviewed.

Installation

Make sure that Netsci is installed and tested: https://github.com/netscianalysis/netsci.git

Activate the Netsci Conda environment

conda activate netsci

The dependency(ies) needed for this repository must be installed manually:

pip install matplotlib
conda install -c conda-forge ambertools

Analyses

Instructions for how to run the analyses used in the paper can be found in the READMEs located in the various directories:

netsci_paper/
  toy_systems/
    README
  proteinG/
    README
  serca/
    README

Citing NetSci

If you use NetSci, or any of the data within this repository, please cite the following paper:

  • Stokely A, Votapka L, Hock M, Teitgen A, McCammon JA, McCullough A, Amaro R, NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-fjrpp This content is a preprint and has not been peer-reviewed.

Copyright

Copyright (c) 2024, Lane Votapka and Andy Stokely

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.