ArticleNucleic acids research2022
CPLM 4.0: an updated database with rich annotations for protein lysine modifications.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.
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Who cites it
53 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Current computational tools for protein lysine acylation site prediction.Briefings in bioinformatics · 2024Pooled it
- Secondary-Amine Relay Enables Lysine-Directed Multicomponent Functionalization of Peptides.JACS Au · 2026Article
- KAT-Net: a hyperbolic routing framework for joint lysine acylation site prediction with shared sequence-structure representations.Briefings in bioinformatics · 2026Article
- Post-translational modifications in metabolic reprogramming: implications for metabolic therapy and immunotherapy in cancer.Signal transduction and targeted therapy · 2026Review
- DeepKbhb: Context-Aware Prediction of Human Lysine β-Hydroxybutyrylation Sites.Journal of chemical information and modeling · 2026Article
- GenPTM: A Generalizable Framework for Protein Post-Translational Modification Information Extraction from the Scientific Literature.Research square · 2026Article
- Regulation of acute myocardial infarction by CircTMCC1 through mitochondrial dysfunction and AMPK/mTOR-driven M1 macrophage polarization: role in QFR assessment.Cell death discovery · 2026Article
- Gravitational and mechanical forces shape mitochondrial translation.Nature communications · 2026Article
- Enhancing the identification of malonylation sites using AlphaFold2 and ensemble learning.Molecular diversity · 2026Article
- A 15-layer multi-omics analysis of gastric cancer ecotypes provides therapeutic insights.Cell reports. Medicine · 2026Article
- StrucPTM: a database of structurally validated protein modifications and their conformational variation.Bioinformatics (Oxford, England) · 2026Article
- Article
- Expanding the Genetic Code with Lysine Aminoacylation.Journal of the American Chemical Society · 2026Article
- Comprehensive analysis of the deleterious nonsynonymous, non-coding SNPs and cancer variants of human aldo-keto reductase type 1 (AKR1C1) protein and their probable association with disease risk and progression: a computational study.Biochemistry and biophysics reports · 2026Article
- Mining lysine post-translational modification sites by integrating protein language model representations with structural context.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- PMADS: an integrated database of curated and proteomics-inferred associations between protein post-translational modifications and drug sensitivity.Nucleic acids research · 2026Article
- PLysPTM-HGNN: predicting lysine PTM sites of proteins using hybrid graph neural networks.BMC bioinformatics · 2026Article
- Exploration of the Immune Microenvironment of Melanoma and Construction of Prognostic Models Based on the Expression Profile of Lysine Crotonylation-Related Genes.International journal of general medicine · 2026Article
- Deep learning model of post-translational modification regulating liquid-liquid phase separation.Communications chemistry · 2025Article
- Mitochondrial hyper-acetylation induced by an engineered acetyltransferase promotes cellular senescence.iScience · 2025Article
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Authors and funding
9 authors.
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Abstract
Here, we reported the compendium of protein lysine modifications (CPLM 4.0, http://cplm.biocuckoo.cn/), a data resource for various post-translational modifications (PTMs) specifically occurred at the side-chain amino group of lysine residues in proteins. From the literature and public databases, we collected 450 378 protein lysine modification (PLM) events, and combined them with the existing data of our previously developed protein lysine modification database (PLMD 3.0). In total, CPLM 4.0 contained 592 606 experimentally identified modification events on 463 156 unique lysine residues of 105 673 proteins for up to 29 types of PLMs across 219 species. Furthermore, we carefully annotated the data using the knowledge from 102 additional resources that covered 13 aspects, including variation and mutation, disease-associated information, protein-protein interaction, protein functional annotation, DNA & RNA element, protein structure, chemical-target relation, mRNA expression, protein expression/proteomics, subcellular localization, biological pathway annotation, functional domain annotation, and physicochemical property. Compared to PLMD 3.0 and other existing resources, CPLM 4.0 achieved a >2-fold increase in collection of PLM events, with a data volume of ∼45GB. We anticipate that CPLM 4.0 can serve as a more useful database for further study of PLMs.
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