PMAP-CutDB proteolytic event database

PMAP-CutDB proteolytic event database catalogs curated proteolytic events and integrates them within the PMAP ecosystem to support analysis and modeling of proteolytic networks and pathways.

Key Features:

• CutDB repository: A community-annotated database containing curated information on over 5,000 proteolytic events.
• Automated annotation pipeline: Generates dynamic "Molecule Pages" with molecular information and enables continuous updating and enrichment of ProteaseDB and SubstrateDB.
• ProfileDB: Captures substrate recognition specificity for various proteases to complement event-level annotations.
• PathwayDB modeling: Models known pathways dynamically using rule-based methods and proposes hypothetical pathways via semi-automated literature culling.
• Protease Toolkit: Provides computational resources for analysis of proteases and proteolytic processes.
• Four-database PMAP ecosystem: Integrates ProteaseDB, SubstrateDB, ProfileDB, and PathwayDB to provide complementary insights into proteolysis.

Scientific Applications:

• Proteolytic network analysis: Use curated event data to analyze relationships and interactions among proteases and substrates.
• Pathway modeling and hypothesis generation: Model known proteolytic pathways and generate hypothetical pathways for experimental follow-up.
• Substrate specificity studies: Investigate protease substrate recognition and specificity using ProfileDB and event annotations.
• Molecular and systems biology research: Support studies in molecular biology, biochemistry, and systems biology that require detailed proteolytic event data.

Methodology:

PMAP-CutDB uses an automated annotation pipeline to generate dynamic "Molecule Pages" and continuously update databases, integrates community annotations, and supports rule-based pathway modeling plus semi-automated literature culling for pathway proposal.