Analyzing Complex Interfaces

This Jupyter notebook analyzes the interface between two proteins, Prot_A and Prot_B, using a multi-step analytical pipeline. The purpose of this pipeline is to provide insights that can inform future interface redesign efforts.

The notebook demonstrates individual steps of the pipeline for a specific use case:

• Prot_A: SARS-CoV-2 spike protein
• Prot_B: Antibody P5A-3C8
• Prot_C: ACE2 PDB entries: 6M0J and 7Z0X

Getting Started

To use this notebook, you will need to install:

• Jupyter Notebook
• PyMOL and download the python module on PATH enviroment
• InterfaceResidues.py

Run the code

Once you have installed the necessary software, you can run the notebook and follow the steps outlined in each section. There are four sections:

• Identify and retrieve the PDB entries 6M0J and 7Z0X.
• Perform structural superimposition of the two complexes to determine the overlap of the binding interfaces using PyMOL.
• Extract the interface residues in each complex using InterfaceResidues within PyMol
• Perform a comparative analysis of the interface residues of SARS-CoV-2 spike protein in the two complexes to identify important residues

The notebook also includes detailed explanations of each step and the underlying concepts and methods used.