UbiBrowser 3.0: towards comprehensively characterizing human ubiquitin ligase-substrate interactions by incorporating ubiquitin chain information.

UbiBrowser 3.0 characterizes 776 human E3 ubiquitin ligase-substrate interactions with detailed ubiquitin chain type associations and cellular effects.

• Why it matters: Understanding the functional diversity of ubiquitination depends on detailed knowledge of ubiquitin chain structures and their regulatory roles, which remains incomplete.
• What they did: The update to UbiBrowser integrates 776 experimentally verified ESI-Ub chain type associations across 8 chain types and 15 cellular effects, expanding the known ESI pairs to 4300, and introduces new chain-centric modules for network visualization and browsing.
• The result: This comprehensive framework enables more precise analysis of ubiquitination mechanisms, supporting hypothesis generation on how ubiquitin chain types influence substrate fate and protein function.