PPIIMoL

PPIIMoL

PPIIMoL is a Python module designed to integrate with PyMOL and automate the detection of polyproline II (PPII) helices in proteins. This tool streamlines structural analysis by identifying characteristic torsional angles (phi and psi) and potential non-canonical hydrogen bonds (Cα-H···O=C).

Developed as part of a Bachelor's Thesis in Computer Engineering in collaboration with the CSIC neuroscience lab.

Features

• 🔍 Automatic detection of PPII segments via phi/psi angle analysis.
• 🧬 Identification of Cα-H···O=C interactions relevant to structural stability.
• 📊 Export of results in CSV format for further analysis.
• 🎨 Direct visualization in PyMOL with customizable color codes.
• 🖱️ Simple GUI based on Tkinter.

Installation

1. Clone this repository:

   git clone https://github.com/silviaenma/PPIIMoL.git

2. Open PyMOL and load the module:

   run PPIIMoL/PPIIMoL.py

Example Usage

# Load the module in PyMOL
run PPIIMoL/PPIIMoL.py

# Detect PPII helices in a PDB file
load 3bog.pdb
ppii_detect()

📂 Results will be automatically exported in a dated folder.

Repository

The project is hosted on GitHub: PPIIMoL on GitHub

License

This project is licensed under the GNU GPLv3.