AIMC Topic: Ubiquitin-Protein Ligases

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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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Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients.

Nature cancer Jan 25, 2021
Cell-line screens create expansive datasets for learning predictive markers of drug response, but these models do not readily translate to the clinic with its diverse contexts and limited data. In the present study, we apply a recently developed tech...
DNA-Binding Proteins Ubiquitin-Protein Ligases Humans Neural Networks, Computer Machine Learning
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DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features.

BMC bioinformatics Nov 12, 2020
BACKGROUND: Circular RNAs (circRNAs) are special noncoding RNA molecules with closed loop structures. Compared with the traditional linear RNA, circRNA is more stable and not easily degraded. Many studies have shown that circRNAs are involved in the ...
Cell Movement Genetic Loci Ubiquitin-Protein Ligases Gene Ontology Protein Interaction Maps Cell Proliferation DNA Helicases RNA, Circular Humans Neural Networks, Computer Cell Line, Tumor
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Differentiating molecular etiologies of Angelman syndrome through facial phenotyping using deep learning.

American journal of medical genetics. Part A Jun 11, 2020
Angelman syndrome (AS) is caused by several genetic mechanisms that impair the expression of maternally-inherited UBE3A through deletions, paternal uniparental disomy (UPD), UBE3A pathogenic variants, or imprinting defects. Current methods of differe...
Genomic Imprinting Ubiquitin-Protein Ligases Maternal Inheritance Angelman Syndrome Uniparental Disomy Humans Adolescent Child, Preschool Phenotype Child Male Female Face Infant Young Adult Deep Learning Adult
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Analysis of differentially expressed genes in rheumatoid arthritis and osteoarthritis by integrated microarray analysis.

Journal of cellular biochemistry Mar 4, 2019
BACKGROUND: Rheumatoid arthritis (RA) and osteoarthritis (OA) were two major types of joint diseases. This study aimed to explore the mechanism underlying OA and RA and analyze their difference by integrated analysis of multiple gene expression data ...
Humans Oligonucleotide Array Sequence Analysis Gene Expression Regulation Gene Expression Profiling Oxidative Phosphorylation Chemokines Protein Interaction Maps Inhibitor of Apoptosis Proteins Ubiquitin-Protein Ligases Gene Regulatory Networks Gene Ontology Arthritis, Rheumatoid Signal Transduction Synovial Membrane Osteoarthritis
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Machine learning identifies interacting genetic variants contributing to breast cancer risk: A case study in Finnish cases and controls.

Scientific reports Sep 3, 2018
We propose an effective machine learning approach to identify group of interacting single nucleotide polymorphisms (SNPs), which contribute most to the breast cancer (BC) risk by assuming dependencies among BCAC iCOGS SNPs. We adopt a gradient tree b...
Finland Case-Control Studies Protein Interaction Mapping Genome-Wide Association Study Estrogen Receptor alpha Gene Regulatory Networks Genetic Predisposition to Disease Humans Base Sequence Prognosis Polymorphism, Single Nucleotide Genome, Human Female Gene Expression Regulation, Neoplastic Risk Breast Neoplasms Support Vector Machine Ubiquitin-Protein Ligases
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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...
Protein Multimerization Expert Systems Mutagenesis, Site-Directed Isoenzymes Ubiquitin Cattle Point Mutation Ubiquitin-Protein Ligases Biocatalysis Ubiquitination Humans Computational Biology Ubiquitin-Conjugating Enzymes Protein Conformation Amino Acid Substitution Animals Cysteine Recombinant Fusion Proteins Models, Molecular Molecular Docking Simulation Binding Sites Iodine Radioisotopes
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The interaction of UBR4, LRP1, and OPHN1 in refractory epilepsy: Drosophila model to investigate the oligogenic effect on epilepsy.

Neurobiology of disease Aug 1, 2025
Refractory epilepsy is an intractable neurological disorder that can be associated with oligogenic/polygenic etiologies. Through trio-based whole-exome sequencing analysis, we identified a clinical case of refractory epilepsy with three candidate gen...
Low Density Lipoprotein Receptor-Related Protein-1 Humans Drosophila Female Drug Resistant Epilepsy Animals GTPase-Activating Proteins Disease Models, Animal Male Animals, Genetically Modified Drosophila Proteins Ubiquitin-Protein Ligases
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[WW domain-containing ubiquitin E3 ligase 1 regulates immune infiltration in tumor microenvironment of ovarian cancer].

Nan fang yi ke da xue xue bao = Journal of Southern Medical University May 20, 2025
OBJECTIVES: To explore the association of the expression of WW domain-containing ubiquitin E3 ligase 1 (WWP1) with immune infiltration in tumor microenvironment (TME) of ovarian cancer.
Humans Prognosis Female Gene Expression Regulation, Neoplastic Tumor Microenvironment Mice, Nude Animals Ovarian Neoplasms Cell Line, Tumor Ubiquitin-Protein Ligases Mice
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ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction.

Briefings in bioinformatics Nov 22, 2024
MOTIVATION: Accurately predicting the degradation capabilities of proteolysis-targeting chimeras (PROTACs) for given target proteins and E3 ligases is important for PROTAC design. The distinctive ternary structure of PROTACs presents a challenge to t...
Proteins Ubiquitin-Protein Ligases Proteolysis Proteolysis Targeting Chimera Humans Neural Networks, Computer
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