ArticleNucleic acids research2013
UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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74 citing papers in PubMed, 108 citations in OpenAlex.
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- Dynamic regulation of the oxidative stress response by the E3 ligase TRIP12.Cell reports · 2025Article
- E3Docker: a docking server for potential E3 binder discovery.Nucleic acids research · 2025Article
- Integrative Multi-Omics Analysis Reveals the Molecular Characteristics, Tumor Microenvironment, and Clinical Significance of Ubiquitination Mechanisms in Lung Adenocarcinoma.International journal of molecular sciences · 2025Article
- PIAS4 regulates pluripotency exit and cell fate commitment in porcine embryonic stem cells.Fundamental research · 2025Article
- Identification and validation of a thirteen-gene signature based on ubiquitin related genes in cervical cancer.Discover oncology · 2025Article
- Pellino 3 E3 ligase promotes starvation-induced autophagy to prevent hepatic steatosis.Science advances · 2025Article
- Multimodal deep learning for predicting protein ubiquitination sites.Bioinformatics advances · 2025Article
- Multi-omics analysis of core E3 ubiquitin ligase identifies prognostic biomarkers associated with immune infiltration and drug sensitivity in lung adenocarcinoma.Journal of Cancer · 2025Article
- An E3 ubiquitin ligase localization screen uncovers DTX2 as a novel ADP-ribosylation-dependent regulator of DNA double-strand break repair.The Journal of biological chemistry · 2024Article
- Article
- Expanding PROTACtable genome universe of E3 ligases.Nature communications · 2023Article
- DUBing Primary Tumors of the Central Nervous System: Regulatory Roles of Deubiquitinases.Biomolecules · 2023Review
- Integrated analysis of the ubiquitination mechanism reveals the specific signatures of tissue and cancer.BMC genomics · 2023Article
- Quantitative measurement of the requirement of diverse protein degradation pathways in MHC class I peptide presentation.Science advances · 2023Article
- Using Activity-Based Proteomics for the Quantification of Deubiquitinases in Animal Tissue.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Identification and characterization of putative biomarkers and therapeutic axis in Glioblastoma multiforme microenvironment.Frontiers in cell and developmental biology · 2023Article
- RoseAP: an analytical platform for gene function ofFrontiers in plant science · 2023Article
- Construction of a prognostic model based on eight ubiquitination-related genesFrontiers in genetics · 2023Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this work, we developed a family-based database of UUCD (http://uucd.biocuckoo.org) for ubiquitin and ubiquitin-like conjugation, which is one of the most important post-translational modifications responsible for regulating a variety of cellular processes, through a similar E1 (ubiquitin-activating enzyme)-E2 (ubiquitin-conjugating enzyme)-E3 (ubiquitin-protein ligase) enzyme thioester cascade. Although extensive experimental efforts have been taken, an integrative data resource is still not available. From the scientific literature, 26 E1s, 105 E2s, 1003 E3s and 148 deubiquitination enzymes (DUBs) were collected and classified into 1, 3, 19 and 7 families, respectively. To computationally characterize potential enzymes in eukaryotes, we constructed 1, 1, 15 and 6 hidden Markov model (HMM) profiles for E1s, E2s, E3s and DUBs at the family level, separately. Moreover, the ortholog searches were conducted for E3 and DUB families without HMM profiles. Then the UUCD database was developed with 738 E1s, 2937 E2s, 46 631 E3s and 6647 DUBs of 70 eukaryotic species. The detailed annotations and classifications were also provided. The online service of UUCD was implemented in PHP + MySQL + JavaScript + Perl.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.