UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase–substrate interactions in eukaryotic species

X Wang, Y Li, M He, X Kong, P Jiang, X Liu… - Nucleic acids …, 2022 - academic.oup.com
As an important post-translational modification, ubiquitination mediates∼ 80% of protein
degradation in eukaryotes. The degree of protein ubiquitination is tightly determined by the …

[HTML][HTML] An integrated bioinformatics platform for investigating the human E3 ubiquitin ligase-substrate interaction network

Y Li, P Xie, L Lu, J Wang, L Diao, Z Liu, F Guo… - Nature …, 2017 - nature.com
The ubiquitination mediated by ubiquitin activating enzyme (E1), ubiquitin conjugating
enzyme (E2), and ubiquitin ligase (E3) cascade is crucial to protein degradation …

UbiHub: a data hub for the explorers of ubiquitination pathways

L Liu, DR Damerell, L Koukouflis, Y Tong… - …, 2019 - academic.oup.com
Motivation Protein ubiquitination plays a central role in important cellular machineries such
as protein degradation or chromatin-mediated signaling. With the recent discovery of the first …

UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase–substrate interactions

Z Li, S Chen, JH Jhong, Y Pang, KY Huang, S Li… - Database, 2021 - academic.oup.com
Ubiquitination is an important post-translational modification, which controls protein turnover
by labeling malfunctional and redundant proteins for proteasomal degradation, and also …

[HTML][HTML] An interaction landscape of ubiquitin signaling

X Zhang, AH Smits, GBA van Tilburg, PWTC Jansen… - Molecular cell, 2017 - cell.com
Intracellular signaling via the covalent attachment of different ubiquitin linkages to protein
substrates is fundamental to many cellular processes. Although linkage-selective ubiquitin …

Identification, analysis, and prediction of protein ubiquitination sites

P Radivojac, V Vacic, C Haynes… - Proteins: Structure …, 2010 - Wiley Online Library
Ubiquitination plays an important role in many cellular processes and is implicated in many
diseases. Experimental identification of ubiquitination sites is challenging due to rapid …

Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features

Z Chen, Y Zhou, Z Zhang, J Song - Briefings in bioinformatics, 2015 - academic.oup.com
Protein ubiquitination is one of the most important reversible post-translational modifications
(PTMs). In many biochemical, pathological and pharmaceutical studies on understanding …

[HTML][HTML] Defining an embedded code for protein ubiquitination

T Jadhav, MW Wooten - Journal of proteomics & bioinformatics, 2009 - ncbi.nlm.nih.gov
It has been more than 30 years since the initial report of the discovery of ubiquitin as an 8.5
kDa protein of unknown function expressed universally in living cells. And still, protein …

[HTML][HTML] UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines

CH Huang, MG Su, HJ Kao, JH Jhong, SL Weng… - BMC systems …, 2016 - Springer
Background The conjugation of ubiquitin to a substrate protein (protein ubiquitylation), which
involves a sequential process–E1 activation, E2 conjugation and E3 ligation, is crucial to the …

[HTML][HTML] Elucidation of E3 ubiquitin ligase specificity through proteome-wide internal degron mapping

Z Zhang, B Sie, A Chang, Y Leng, C Nardone… - Molecular cell, 2023 - cell.com
The ubiquitin-proteasome system plays a critical role in biology by regulating protein
degradation. Despite their importance, precise recognition specificity is known for a few of …