AIMC Topic: Ubiquitin

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NMR spectrum reconstruction as a pattern recognition problem.

Journal of magnetic resonance (San Diego, Calif. : 1997) Nov 24, 2022
A new deep neural network based on the WaveNet architecture (WNN) is presented, which is designed to grasp specific patterns in the NMR spectra. When trained at a fixed non-uniform sampling (NUS) schedule, the WNN benefits from pattern recognition of...
Magnetic Resonance Imaging Nuclear Magnetic Resonance, Biomolecular Magnetic Resonance Spectroscopy Ubiquitin Neural Networks, Computer
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Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.

BMC biology Jul 14, 2022
BACKGROUND: Degrons are short linear motifs, bound by E3 ubiquitin ligase to target protein substrates to be degraded by the ubiquitin-proteasome system. Mutations leading to deregulation of degron functionality disrupt control of protein abundance d...
Deep Learning Proteome Ubiquitin-Protein Ligases Proteolysis Ubiquitin
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Computed structures of core eukaryotic protein complexes.

Science (New York, N.Y.) Dec 10, 2021
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...
Computer Simulation Chromosome Segregation Ligases Multiprotein Complexes Acyltransferases Homologous Recombination Protein Conformation Saccharomyces cerevisiae Ubiquitin Protein Interaction Mapping Saccharomyces cerevisiae Proteins DNA Repair Protein Biosynthesis Ribosomes Proteome Membrane Proteins Deep Learning Evolution, Molecular Protein Interaction Maps Models, Molecular Computational Biology
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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...
Cell Line, Tumor Proteomics Proteome Signal Transduction Humans Neural Networks, Computer Time Factors Ubiquitin Ubiquitination Ubiquitin-Specific Peptidase 7 Tandem Mass Spectrometry HCT116 Cells Jurkat Cells Substrate Specificity
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A Machine Learning Protocol for Predicting Protein Infrared Spectra.

Journal of the American Chemical Society Oct 30, 2020
Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive quantum-mechanical calculations i...
Proteins Amides Quantum Theory Ubiquitin Spectrophotometry, Infrared Protein Structure, Secondary Protein Folding Machine Learning Temperature Peptides
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Discovery of gene module acting on ubiquitin-mediated proteolysis pathway by co-expression network analysis for endometriosis.

Reproductive biomedicine online Oct 14, 2020
RESEARCH QUESTION: Is abnormal gene module expression in the eutopic endometrium related to the occurrence of endometriosis?
Ubiquitin Gene Regulatory Networks Endometriosis Proteolysis Humans Neural Networks, Computer Female
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Machine Learning Driven Analysis of Large Scale Simulations Reveals Conformational Characteristics of Ubiquitin Chains.

Journal of chemical theory and computation Apr 7, 2020
Understanding the conformational characteristics of protein complexes in solution is crucial for a deeper insight in their biological function. Molecular dynamics simulations performed on high performance computing plants and with modern simulation t...
Machine Learning Molecular Dynamics Simulation Protein Conformation Ubiquitin
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A novel method for the rapid detection of post-translationally modified visinin-like protein 1 in rat models of brain injury.

Brain injury Dec 28, 2017
BACKGROUND: Although elevated serum levels of visinin-like protein 1 (VILIP-1), a neuron-specific calcium sensor protein, are associated with ischaemic stroke, only a single study has evaluated VILIP-1 as a biomarker of traumatic brain injury (TBI). ...
Ubiquitin Disease Models, Animal Cohort Studies Brain Injuries Humans HEK293 Cells Linear Models Time Factors Animals Cerebral Cortex Rats Male Immunoprecipitation Rats, Sprague-Dawley Neurocalcin
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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...
Expert Systems Biocatalysis Protein Conformation Cysteine Ubiquitin-Protein Ligases Amino Acid Substitution Recombinant Fusion Proteins Cattle Computational Biology Models, Molecular Iodine Radioisotopes Humans Animals Molecular Docking Simulation Ubiquitin-Conjugating Enzymes Ubiquitination Binding Sites Protein Multimerization Mutagenesis, Site-Directed Isoenzymes Ubiquitin Point Mutation
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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....
Proteomics Proteome Mass Spectrometry Ubiquitin Machine Learning Models, Molecular Protein Domains Ubiquitination Software Amino Acid Sequence Amino Acid Motifs Datasets as Topic Sequence Analysis, Protein Lysine
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