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Custom Software • AI • Data Engineering • Bioinformatics

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CaviDB: Protein Cavity Database and Analytics Platform

 

Overview

Developed an open-access, web-based database integrating structural and conformational data on protein cavities, combining multiple cavity detection algorithms with protein sequence and functional annotations. The platform enables researchers to explore dynamic cavity features across protein conformers, supporting drug design and fundamental protein structure-function studies. 


 

Key Features

  • Database of ∼927,000 proteins and over 36 million characterized cavities
  • Integration of multiple cavity detection tools for robust feature extraction
  • Linking of proteins to conformers to analyze conformational cavity changes
  • Advanced search and comparison functionalities for cavity properties
  • User-friendly web interface accessible to bioinformaticians and biologists
  • Exportable datasets for downstream drug discovery applications
     

Add-ons

  • Custom data curation workflows for NGO and collaborating researchers
  • Visualization tools for cavity dynamics and chemical properties
  • API for external software integration and automated queries
     

Results

  • Facilitated new insights into protein-ligand interactions and drug target identification
  • Supported the global research community with a comprehensive structural resource
  • Enhanced understanding of protein structure-function relationships
     

Deployment
Deployed on NGO-managed cloud infrastructure, ensuring open access, data security, and compliance with institutional data policies.

Client: Non-profit Research NGO specializing in Structural Biology and Bioinformatics 

Timeline: 8 months (development, testing, deployment), ongoing maintenance until Q4 2024 

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