UbiNe

UbiNe integrates experimentally verified protein ubiquitylation sites, manually curated E1/E2/E3 enzyme annotations, and protein–protein interaction networks to enable analysis of E3 ubiquitin ligase–substrate regulatory networks.

Key Features:

• Extensive database: Contains 43,948 experimentally verified ubiquitylation sites from 14,692 human proteins.
• Curated enzyme annotations: Includes manually curated information on 499 E3 ligases, two E1 activating enzymes, and 46 E2 conjugating enzymes.
• Protein–protein interaction integration: Integrates 430,530 protein–protein interactions to represent regulatory networks among E3 ligases and ubiquitylated proteins.
• Substrate inference: Identifies potential substrates for specific E3 ligases based on interaction data and substrate motifs.

Scientific Applications:

• E3–substrate network analysis: Enables reconstruction and analysis of E3 ubiquitin ligase–substrate regulatory networks.
• Substrate identification: Facilitates nomination of candidate substrates for specific E3 ligases using integrated interaction and motif information.
• Regulatory mechanism elucidation: Supports elucidation of ubiquitylation-based regulatory schemes, including examples involving Mdm2 regulation of p53.
• Cancer-related ubiquitylation studies: Provides data and network context for investigating ubiquitylation of tumor proteins such as p63 and p73.
• Hypothesis generation and preliminary analyses: Serves as a resource for generating hypotheses and conducting preliminary analyses of ubiquitylation-mediated cellular processes and potential therapeutic targets.

Methodology:

Integration of experimentally verified ubiquitylation sites with manually curated enzyme annotations and protein–protein interaction networks, and identification of candidate E3 substrates based on interaction data and substrate motifs.