Knowledge-based potentials for new coarse-grained protein model

Goals & Theory

The main goals of the project was to

• determine the initial parameters for the potentials
• examine some possible ways to reduce the number of these parameters

The model

The potentials

• Ramachandran Map potential
• Side-Chain united atom interaction potentials

Way to reduce # of parameters

• Reduced SVD
• GMM (Gaussian Mixture Model)

File Structure

Directories:

• my
• my_utilities - files containing classes & functions used in scripts and notebooks in top level directory
• setup

Also

• 0_S_[name].py - scripts
• 1_D_[name].py - jupyter notebooks containing actual plots and analysis

Setup

Python vesion: python 3.7

pip install -r ./setup/requirements.txt

Credits

• Multiple files and statistics used in this project have been obtained using Bioshell package
• Excluded volume masks have been created with help of Pyrosetta

Author

Piotr Śmieja, 2023