ArticleNature communications2024
A protein sequence-based deep transfer learning framework for identifying human proteome-wide deubiquitinase-substrate interactions.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Deep learning-driven decoding of ubiquitination: from regulatory mechanisms to targeted protein degradation.Biology direct · 2026Review
- Interpretable deep learning framework for mapping E3-substrate binding interfaces.Nature communications · 2026Article
- Opening the black box: insights into ubiquitin-mediated control of innate antiviral immunity and AI-enhanced therapeutics.Frontiers in immunology · 2026Review
- Phylogenetic Domain Adaption for Linear B-Cell Epitope Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Integrative Omics Reveals Glutamine Catabolism-Driven Apoptotic Suppression in Monocytes upon Mechanical Unloading.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- AI4Protein: transforming the future of protein design.Science China. Life sciences · 2025Review
- Deubiquitinase OTUD7B stabilizes HNF4α to alleviate pressure overload-induced cardiac hypertrophy by regulating fatty acid oxidation and inhibiting ferroptosis.Biomarker research · 2025Article
- Multi-omics decodes host-specific and environmental microbiome interactions in sepsis.Frontiers in microbiology · 2025Review
- The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.Journal of proteome research · 2024Review
- A protein sequence-based deep transfer learning framework for identifying human proteome-wide deubiquitinase-substrate interactions.Nature communications · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Protein ubiquitination regulates a wide range of cellular processes. The degree of protein ubiquitination is determined by the delicate balance between ubiquitin ligase (E3)-mediated ubiquitination and deubiquitinase (DUB)-mediated deubiquitination. In comparison to the E3-substrate interactions, the DUB-substrate interactions (DSIs) remain insufficiently investigated. To address this challenge, we introduce a protein sequence-based ab initio method, TransDSI, which transfers proteome-scale evolutionary information to predict unknown DSIs despite inadequate training datasets. An explainable module is integrated to suggest the critical protein regions for DSIs while predicting DSIs. TransDSI outperforms multiple machine learning strategies against both cross-validation and independent test. Two predicted DUBs (USP11 and USP20) for FOXP3 are validated by "wet lab" experiments, along with two predicted substrates (AR and p53) for USP22. TransDSI provides new functional perspective on proteins by identifying regulatory DSIs, and offers clues for potential tumor drug target discovery and precision drug application.
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Registered trials
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