soaPDB

soaPDB manages saved searches and alerts for the Protein Data Bank (PDB), enabling systematic storage and retrieval of search queries and results to support structural biology and bioinformatics research.

Key Features:

• Saved Searches: Store and organize PDB search criteria and their resulting entries for later retrieval.
• Search Result Archiving: Persist search results and associated metadata in a relational database for reproducible tracking.
• Automatic Email Alerts: Send automatic email notifications when new or updated PDB entries match saved searches.
• Relational Database Backend: Use a relational database to manage stored queries, results, and related metadata.
• PDB Monitoring: Track changes and additions to Protein Data Bank entries relevant to saved queries.

Scientific Applications:

• Drug discovery: Maintain awareness of newly deposited PDB structures that can inform structure-based drug design.
• Protein engineering: Monitor structural updates and new homologs in the PDB that are relevant to engineering efforts.
• Molecular modeling: Provide up-to-date structural coordinates from the PDB for modeling and simulation workflows.
• Bioinformatics and structural biology workflows: Integrate PDB change-tracking into analyses that depend on current structural data.

Methodology:

Implemented using the Ruby on Rails framework with a relational database backend to store and manage search queries and results.