3D structure analysis and visualization Notebook

Overview

• This Jupyter Notebook is a powerful tool for analyzing and visualizing the 3D structure of macromolecules. It allows users to input a PDB ID, fetches the corresponding structural data, and extracts detailed information from the CIF file using Biopython. The notebook provides insights into binding sites and other structural features, making it ideal for researchers and students in structural biology and bioinformatics.

Case Study

• As a demonstration, the notebook includes a case study on the Keap1-Kelch domain, showcasing a published study that explores lignans as activators of Keap1. This highlights the notebook's utility in real-world applications of macromolecular analysis. You can access our published article, The promising antioxidant effects of lignans: Nrf2 activation comes into view

Features

• User-friendly Interface: Input a PDB ID, and the notebook does the rest.
• Data Extraction: Extracts binding site information and other useful structural data from CIF files.
• Visualization: Visualize 3D structures of macromolecules.
• Biopython Integration: Utilizes the powerful Biopython library for structural data processing.
• Case Study Included: Example use case focused on the Keap1-Kelch domain and lignan activators.

---

Prerequisites

• Jupyter Notebook or JupyterLab
• Required Python Libraries:
• biopython
• nglview
• numpy

---

Installation

1. Clone the repository:

git clone https://github.com/YourUsername/3D-structure-analysis.git

2. Navigate to the project directory:

cd 3D-Structure-Analysis

3. Launch the Jupyter Notebook:

jupyter notebook

Usage

• Run the notebook.
• Enter a PDB ID when prompted.
• View and analyze:
• Binding sites.
• Structural features.
• 3D visualization of the macromolecule.