ProModb

ProModb catalogs computationally generated whole-cell protein-protein interaction network-based functional modules and their spatial localizations to support analysis of cellular organization and modular pharmacology.

Key Features:

• Functional Module Identification: Identifies and characterizes functional and structural aspects of biological networks at the cellular level, enabling detection of evolutionary signals.
• Integration with KEGG Pathway Database: Maps modules to KEGG pathway annotations and generates spatially localized protein modules for organisms indexed in the KEGG genome database.
• Real-Time Web Scraping and Data Integration: Uses ProFuM-Cell to perform real-time web scraping of experimentally verified online sources to construct Protein Locality Graphs and aggregate interaction data.
• Aggregation of Experimental Interaction and Pathway Data: Aggregates experimental interaction data from multiple interaction databases and pathway maps to produce spatial locality-based protein modules.

Scientific Applications:

• Modular Pharmacology: Supports modular pharmacology approaches for diagnosing, preventing, and treating diseases by targeting functional modules within protein-protein interaction networks.
• Evolutionary Network Analysis: Enables comparative and evolutionary analyses of network organization by characterizing conserved and divergent functional modules across organisms.

Methodology:

Constructs Protein Locality Graphs and clusters cellular-level functional units using ProFuM-Cell real-time web scraping of experimentally verified online sources, with module mapping integrated to KEGG pathway data.