Protein Structure Database

An interactive web-based application to explore protein 3D structures and ligand molecular structures using publicly available biological databases.

The project is designed for students and beginners in bioinformatics to understand protein structures without dealing with complex file formats.

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Features

• Search proteins using PDB ID
• Interactive 3D protein structure visualization (Mol* / iCn3D)
• Display ligand molecular structures using PubChem (CID-based)
• Structured SQLite protein database
• Admin-only access for data ingestion
• Clean multi-page Streamlit interface

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Data Sources

• RCSB Protein Data Bank (PDB) – protein structure metadata
• NCBI iCn3D / Mol* – 3D structure visualization
• PubChem – ligand molecular structures (2D/3D)

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Tech Stack

• Python
• Streamlit (frontend & UI)
• SQLite (database)
• REST APIs (RCSB, PubChem)
• HTML iFrames (3D visualization)

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Project Structure

protein_structuredb/ │
├── home.py # Home page
├── protein_structure.db # SQLite database
├── requirements.txt
├── pages/
│ ├── 1_Admin.py # Admin panel (add proteins)
│ ├── 2_3D_Structure.py # 3D structure viewer
│ ├── 3_Search.py # Protein search & detail view

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How to Run the Project

1️ Clone the repository

git clone https://github.com/shad921z/protein-structure-database.git
cd protein-structure-database 

2️ Install dependencies

pip install -r requirements.txt

3️ Run the application

streamlit run app.py

Admin Access

The admin panel is protected using a session-based password gate. Only the admin can add new protein data to the database.

Intended Audience

• Life science students
• Beginners in bioinformatics
• Educators demonstrating protein structures
• Developers exploring biology-related applications

NEW UPDATES

• Added Update and Delete functions in the admin menu
• Improved overall UI
• Improved 3d structure view
• Improved Navigation
• Fixed ligand and molecular structure image issue

Future Improvements

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Protein-Structure-Database

An interactive protein structure database that retrieves data from public biological APIs, stores it in a relational database, and visualizes protein and ligand structures using embedded 3D viewers.

30ae89b (commit)