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THGLab / MCSCE

Monte Carlo Side Chain Entropy package for generating side chain packing for fixed protein backbone
MIT License
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MCSCE - Sidechain packing library

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Monte Carlo Side Chain Entropy package for generating side chain packing for fixed protein backbone.

Updated supports for phosphorated residues and other listed modifications; other ptms in development.

Phosphoralytion(unprotonated, protonated)

Methylation

N6-carboxylysine

Hydroxylation

v0.1.0

References

1.Lin, M. S., Fawzi, N. L. & Head-Gordon, T. Hydrophobic Potential of Mean Force as a Solvation Function for Protein Structure Prediction. Structure 15, 727–740 (2007).

  1. Bhowmick, A. & Head-Gordon, T. A Monte Carlo Method for Generating Side Chain Structural Ensembles. Structure 23, 44–55 (2015).

How to Install

  1. Clone this repository::

    git clone https://github.com/THGLab/MCSCE

  2. Navigate to the new folder::

    cd MCSCSE

  3. Create a dedicated Conda environment with the needed dependencies::

    conda env create -f requirements.yml

  4. Install MCSCE package manually::

    python setup.py develop --no-deps

  5. To update to the latest version::

    git pull

How to Use

In your terminal window run for help::

mcsce -h

How to Contribute

Contribute to this project following the instructions in docs/CONTRIBUTING.rst_ file.

.. _docs/CONTRIBUTING.rst: https://github.com/THGLab/MCSCE/blob/master/docs/CONTRIBUTING.rst