AIMC Topic: Ubiquitination

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PrUb-EL: A hybrid framework based on deep learning for identifying ubiquitination sites in Arabidopsis thaliana using ensemble learning strategy.

Analytical biochemistry Oct 4, 2022
Identification of ubiquitination sites is central to many biological experiments. Ubiquitination is a kind of post-translational protein modification (PTM). It is a key mechanism for increasing protein diversity and plays a vital role in regulating c...
Dipeptides Ubiquitination Arabidopsis Ubiquitinated Proteins Deep Learning Amino Acids
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An Ensemble Deep Learning based Predictor for Simultaneously Identifying Protein Ubiquitylation and SUMOylation Sites.

BMC bioinformatics Oct 24, 2021
BACKGROUND: Several computational tools for predicting protein Ubiquitylation and SUMOylation sites have been proposed to study their regulatory roles in gene location, gene expression, and genome replication. However, existing methods generally rely...
Ubiquitination Amino Acid Sequence Lysine Sumoylation Deep Learning
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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...
Deep Learning Ubiquitin-Protein Ligases Ubiquitination
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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...
Humans Neural Networks, Computer HCT116 Cells Jurkat Cells Substrate Specificity Ubiquitin-Specific Peptidase 7 Ubiquitin Ubiquitination Proteome Signal Transduction Tandem Mass Spectrometry Time Factors Cell Line, Tumor Proteomics
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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...
Mice Computational Biology Proteome Neural Networks, Computer Software Animals Ubiquitination Arabidopsis Protein Processing, Post-Translational Amino Acids Yeasts Humans
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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...
Deep Learning Proteomics Proteome Ubiquitinated Proteins Lysine Ubiquitination Humans Neural Networks, Computer Software
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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...
Isoenzymes Point Mutation Ubiquitin-Conjugating Enzymes Humans Animals Amino Acid Substitution Computational Biology Recombinant Fusion Proteins Models, Molecular Binding Sites Molecular Docking Simulation Ubiquitination Cattle Protein Conformation Protein Multimerization Mutagenesis, Site-Directed Iodine Radioisotopes Cysteine Expert Systems Ubiquitin Ubiquitin-Protein Ligases Biocatalysis
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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 ...
Lysine Algorithms Binding Sites Protein Processing, Post-Translational Support Vector Machine Ubiquitination Machine Learning Proteins Databases, Protein
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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....
Sequence Analysis, Protein Proteome Ubiquitin Amino Acid Sequence Mass Spectrometry Ubiquitination Datasets as Topic Models, Molecular Amino Acid Motifs Lysine Protein Domains Machine Learning Software Proteomics
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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...
Gene Expression Profiling Gene Expression Regulation, Neoplastic Humans Ubiquitination Transcriptome Squamous Cell Carcinoma of Head and Neck Laryngeal Neoplasms Carcinoma, Squamous Cell Gene Regulatory Networks Biomarkers, Tumor
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