MCSCE - Sidechain packing library

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)

• SER: SEP S1P
• THR: TPO T1P
• TYR: PTR Y1P
• HID: H2D H1D (opt from SIDEpro)
• HIE: H2E H1E (opt from SIDEpro)

Acetylation

• LYS: ALY

Methylation

• LYS: M3L

N6-carboxylysine (opt from SIDEpro)

• LYS: KCX

Hydroxylation (opt from SIDEpro)

• PRO: HYP

Important: while MCSCE handles multiple chains, each residue should have unique residue ids; otherwise the energy function may have unexpected behaviors.

v0.1.2

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).

2. 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.