HProteome-BSite

Public repository showcasing the source code for the HProteome-BSite database.

Project

Visit the live database: https://galaxy.seoklab.org/hproteome-bsite/database/

Screenshot of the HProteome-BSite web interface

📋 Project Overview

HProteome-BSite is a comprehensive database and web interface for exploring human-proteome-wide binding site and ligand information. This repository showcases the Django-based web application source code that powers the database interface.

Key Features

• Comprehensive Database: Proteome-wide binding site information with over 20,000+ protein domains
• Interactive Web Interface: User-friendly search and visualization with molecular structure viewing
• Easy-docking via Web-server: Docking predicted ligands to binding sites is possible through HProteome-BSite web server
• Molecular Visualization: Integration with MolStar for 3D structure viewing
• Bulk Download: Comprehensive data export capabilities

Binding Site Prediction Tool: GalaxySite2

• Provided predictions of binding sites and ligands were made using GalaxySite, a template based binding site prediction method. Upon building HProteome-BSite, I have updated GalaxySite both database- and algorithm-wise.
• GalaxySite2 repository: https://github.com/j2ho/GalaxySite2.git (dependent on Galaxy and GalaxyPipe packages)
• Outline of GalaxySite binding prediction on the AlphaFold human structure database. Details of this method can be found in the paper cited at the end.

📁 Repository Structure

hproteome-bsite-pub/
├── database/                   # Main Django application
│   ├── models.py              # Database models and schema
│   ├── views.py               # Application views and logic
│   ├── urls.py                # URL routing
│   ├── templates/             # HTML templates
│   └── migrations/            # Database migration files
├── sitedb/                    # Django project configuration
│   ├── settings.py            # Project settings
│   ├── urls.py               # Main URL configuration
│   └── wsgi.py               # WSGI application entry point
└── manage.py                 # Django management 

⚠️ Repository Notes

This is a showcase repository containing the core source code. Please note:

• Static files excluded: Production static files (CSS, JS, images) are not included
• Security files removed: Sensitive configuration and credentials have been removed
• Live deployment: The fully functional version is available at the link above
• Data files: Actual predictions (PDB files for complex structures) are excluded

Contact

For questions about the HProteome-BSite database, please visit the official website.

Citation

If you use HProteome-BSite (DB or docking) and/or GalaxySite in your research, please cite:

Paper: HProteome-BSite: A comprehensive database of human proteome-wide binding sites

Website: https://galaxy.seoklab.org/hproteome-bsite/database/

@article{hproteome_bsite_2022,
    title={HProteome-BSite: A comprehensive database of human proteome-wide binding sites},
    author={Jiho Sim, Sohee Kwon, Chaok Seok*},
    journal={Nucleic Acids Research},
    year={2022},
    doi={10.1093/nar/gkac873}
}

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Note: This repository contains the core source code only. For the full functionality of the HProteome-BSite database, additional configuration and static files are required.