AIMC Topic: Ubiquitination
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A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction.
BMC bioinformatics
Oct 18, 2021
BACKGROUND: Ubiquitylation is an important post-translational modification of proteins that not only plays a central role in cellular coding, but is also closely associated with the development of a variety of diseases. The specific selection of subs...
Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale.
Nature communications
Sep 13, 2021
Mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with dat...
Computational identification of ubiquitination sites in Arabidopsis thaliana using convolutional neural networks.
Plant molecular biology
Feb 1, 2021
We developed two CNNs for predicting ubiquitination sites in Arabidopsis thaliana, demonstrated their competitive performance, analyzed amino acid physicochemical properties and the CNN structures, and predicted ubiquitination sites in Arabidopsis. A...
DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins.
BMC bioinformatics
Feb 18, 2019
BACKGROUND: Protein ubiquitination occurs when the ubiquitin protein binds to a target protein residue of lysine (K), and it is an important regulator of many cellular functions, such as signal transduction, cell division, and immune reactions, in eu...
modeling of the cryptic E2∼ubiquitin-binding site of E6-associated protein (E6AP)/UBE3A reveals the mechanism of polyubiquitin chain assembly.
The Journal of biological chemistry
Sep 18, 2017
To understand the mechanism for assembly of Lys-linked polyubiquitin degradation signals, we previously demonstrated that the E6AP/UBE3A ligase harbors two functionally distinct E2∼ubiquitin-binding sites: a high-affinity Site 1 required for E6AP Cys...
Point Mutation
Humans
Ubiquitin-Conjugating Enzymes
Ubiquitination
Expert Systems
Binding Sites
Protein Multimerization
Biocatalysis
Mutagenesis, Site-Directed
Protein Conformation
Isoenzymes
Ubiquitin
Amino Acid Substitution
Recombinant Fusion Proteins
Computational Biology
Cysteine
Models, Molecular
Ubiquitin-Protein Ligases
Iodine Radioisotopes
Animals
Molecular Docking Simulation
Cattle
Positive-Unlabeled Learning for Pupylation Sites Prediction.
BioMed research international
Aug 7, 2016
Pupylation plays a key role in regulating various protein functions as a crucial posttranslational modification of prokaryotes. In order to understand the molecular mechanism of pupylation, it is important to identify pupylation substrates and sites ...
UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.
BMC systems biology
Jan 11, 2016
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 regulation of protein function and activity in eukaryotes....
Transcriptomics-based exploration of ubiquitination-related biomarkers and potential molecular mechanisms in laryngeal squamous cell carcinoma.
BMC medical genomics
May 12, 2025
BACKGROUND: One of the most common and prevalent cancers is laryngeal squamous cell carcinoma (LSCC), which poses a great threat to the life and health of the patient. Nonetheless, it has been demonstrated that ubiquitination is crucial for the devel...
Correlation Network Analysis Provides Important Modules and Pathways for Human Hyperlipidemia.
Critical reviews in eukaryotic gene expression
Jan 1, 2019
Hyperlipidemia casts great threats to humans around the world. The systemic co-expression and function enrichment analysis for this disease is limited to date. This study was to identify co-expression modules to explore hyperlipidemia-associated func...
ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives.
Bioinformatics (Oxford, England)
Mar 1, 2017
MOTIVATION: Numerous ubiquitination sites remain undiscovered because of the limitations of mass spectrometry-based methods. Existing prediction methods use randomly selected non-validated sites as non-ubiquitination sites to train ubiquitination sit...
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