ArticleBioinformatics (Oxford, England)2023
PTMint database of experimentally verified PTM regulation on protein-protein interaction.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 25 citations in OpenAlex.
- Evidence for the Formation of Metabolons Surrounding the Pyruvate Node in the Supercritical COACS omega · 2026Article
- Learning the PTM code through a coarse-to-fine mechanism-aware framework.Nature communications · 2026Article
- Post-translational Modifications in Proteins: Prediction Methods, Biological Functions, and Diseases.MedComm · 2026Review
- PTMs_Closed_Search: Multiple Post-Translational Modification Closed Search Using Reduced Search Space and Transferred FDR.Proteomes · 2026Article
- PMADS: an integrated database of curated and proteomics-inferred associations between protein post-translational modifications and drug sensitivity.Nucleic acids research · 2026Article
- Exercise-specific post-translational modification signatures: unveiling precise regulatory mechanisms of molecular exercise language and cellular adaptation.Frontiers in sports and active living · 2026Review
- Deep learning model of post-translational modification regulating liquid-liquid phase separation.Communications chemistry · 2025Article
- Review
- DeepPhosPPI: a deep learning framework with attention-CNN and transformer for predicting phosphorylation effects on protein-protein interactions.Briefings in bioinformatics · 2025Article
- Applying a Conservation-Based Approach for Predicting Novel Phosphorylation Sites in Eukaryotes and Evaluating Their Functional Relevance.Journal of proteome research · 2025Article
- PTM-Mamba: a PTM-aware protein language model with bidirectional gated Mamba blocks.Nature methods · 2025Article
- A Mass Spectrometry-Based Proteomics Workflow for Concurrent Profiling of Protein Thiol Oxidation and Phosphorylation.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Large Language Model (LLM)-Based Advances in Prediction of Post-translational Modification Sites in Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Post-translational modification prediction via prompt-based fine-tuning of a GPT-2 model.Nature communications · 2024Article
- Chemical proteomics approaches for protein post-translational modification studies.Biochimica et biophysica acta. Proteins and proteomics · 2024Review
- Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts.Microbial cell (Graz, Austria) · 2024Article
- Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
motivationPost-translational modification (PTM) is an important biochemical process. which includes six most well-studied types: phosphorylation, acetylation, methylation, sumoylation, ubiquitylation and glycosylation. PTM is involved in various cell signaling pathways and biological processes. Abnormal PTM status is closely associated with severe diseases (such as cancer and neurologic diseases) by regulating protein functions, such as protein-protein interactions (PPIs). A set of databases was constructed separately for PTM sites and PPI; however, the resource of regulation for PTM on PPI is still unsolved.
resultsHere, we firstly constructed a public accessible database of PTMint (PTMs that are associated with PPIs) (https://ptmint.sjtu.edu.cn/) that contains manually curated complete experimental evidence of the PTM regulation on PPIs in multiple organisms, including Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Currently, the first version of PTMint encompassed 2477 non-redundant PTM sites in 1169 proteins affecting 2371 protein-protein pairs involving 357 diseases. Various annotations were systematically integrated, such as protein sequence, structure properties and protein complex analysis. PTMint database can help to insight into disease mechanism, disease diagnosis and drug discovery associated with PTM and PPI. AVAILABILITY AND IMPLEMENTATION: PTMint is freely available at: https://ptmint.sjtu.edu.cn/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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 Socratic graph.