Contact Density

This repository contains a Python script to calculate the contact density of a protein conformation with respect to its native conformation. It first aligns the given protein structure to the native structure and then calculates their contact density.

Prerequisites

To run this script, you'll need to have the following installed:

• Python 3.6 or higher
• Biopython library

You can install Biopython using pip:

pip install biopython

Usage

1. Clone the repository to your local machine:

git clone [email protected]:shalinis602/Contact-Density.git
cd Contact-Density

2. Place your protein conformation PDB files in the repository directory. Ensure you have two PDB files:

• One for the given protein conformation.
• One for the native protein conformation.

3. Run the script:

python contact_density.py

4. Follow the prompts to input the filenames of your protein conformation and native structure PDB files.

Example

Here is an example of how to use the script:

Enter the filename for the conformation structure (e.g., conformation.pdb): markov_rf_4988.pdb
Enter the filename for the native structure (e.g., native.pdb): native.pdb
Contacts in given protein conformation = 100
Contacts in native protein conformation = 120
Common contacts = 80
Contact density % = 66.67

How It Works

The script performs the following steps:

1. Read Coordinates: It reads the alpha carbon (CA) atom coordinates from the given PDB files.
2. Align Structures: It aligns the given protein conformation to the native structure using Biopython's Superimposer.
3. Calculate Contacts: It calculates the contacts within each structure based on a distance threshold (default is 6.0 Å).
4. Calculate Common Contacts: It calculates the number of common contacts between the two structures.
5. Compute Contact Density: It computes the contact density as the percentage of common contacts relative to the total contacts in the native structure.

Contributing

If you find any issues or have suggestions for improvements or expanding the project, feel free to open an issue or submit a pull request.

Acknowledgements

This script uses the Biopython library for PDB parsing and structure manipulation. Biopython is an open-source project available here.