UbiBrowser 2.0

UbiBrowser 2.0 provides an integrated database of known and predicted interactions between ubiquitin ligases (E3s), deubiquitinases, and their substrates to support analysis of ubiquitination-mediated protein regulation.

Key Features:

• Extensive data collection: Manually curated 4,068 known E3–substrate interactions (ESIs) and 967 deubiquitinase–substrate interactions (DSIs), and computationally predicts approximately 2.2 million highly confident ESIs/DSIs.
• Expanded species coverage: Includes curated and predicted interactions across 39 eukaryotic organisms.
• Simultaneous exploration: Enables investigation of both upstream E3 ligases and deubiquitinases for specific substrates.
• Uniform confidence scoring: Applies a standardized confidence scoring system to rank predicted ESIs and DSIs.
• Scale expansion: Total data volume increased by more than 210-fold compared to the predecessor.

Scientific Applications:

• Ubiquitination dynamics: Supports research into the balance between ubiquitin ligase-mediated ubiquitination and deubiquitinase-mediated deubiquitination.
• Protein degradation regulation: Aids analysis of regulatory mechanisms governing ubiquitin-dependent protein degradation pathways.
• Target discovery: Facilitates identification of candidate ubiquitination-related drug targets in diseases with dysregulated ubiquitination.

Methodology:

Manual curation of 4,068 ESIs and 967 DSIs, computational prediction of approximately 2.2 million ESIs/DSIs across 39 organisms, and application of a standardized confidence scoring system to rank predicted interactions.