ArticleNucleic acids research2015
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Current computational tools for protein lysine acylation site prediction.Briefings in bioinformatics · 2024Pooled it
- Post‑translational modification‑governed immune states in cancer immunity: Biomarker implications for checkpoint competence, tumor visibility and immunotherapy resistance (Review).International journal of oncology · 2026Review
- Learning the PTM code through a coarse-to-fine mechanism-aware framework.Nature communications · 2026Article
- A spatial and temporal atlas of tubulin isotype expression during neural crest EMT.bioRxiv : the preprint server for biology · 2026Article
- Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome.Journal of cardiovascular development and disease · 2026Review
- Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.Proteomics · 2025Review
- Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics.Journal of proteome research · 2025Article
- Posttranslational Modifications ofPharmacological reviews · 2024Review
- GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs.Nucleic acids research · 2024Article
- Decoding glycosylation potential from protein structure across human glycoproteins with a multi-view recurrent neural network.bioRxiv : the preprint server for biology · 2024Article
- Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences.Database : the journal of biological databases and curation · 2024Review
- Decoding Ubiquitin Modifications by Mass Spectrometry.Advances in experimental medicine and biology · 2024Review
- AutophagyNet: high-resolution data source for the analysis of autophagy and its regulation.Autophagy · 2024Article
- Making proteomics accessible: RokaiXplorer for interactive analysis of phospho-proteomic data.Bioinformatics advances · 2024Article
- A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction.Genomics, proteomics & bioinformatics · 2023Review
- qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast.Nucleic acids research · 2023Article
- PTMint database of experimentally verified PTM regulation on protein-protein interaction.Bioinformatics (Oxford, England) · 2023Article
- Prediction of Kinase-Substrate Associations Using The Functional Landscape of Kinases and Phosphorylation Sites.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2023Article
- The Four Homeostasis Knights: In Balance upon Post-Translational Modifications.International journal of molecular sciences · 2022Review
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The post-translational regulation of proteins is mainly driven by two molecular events, their modification by several types of moieties and their interaction with other proteins. These two processes are interdependent and together are responsible for the function of the protein in a particular cell state. Several databases focus on the prediction and compilation of protein-protein interactions (PPIs) and no less on the collection and analysis of protein post-translational modifications (PTMs), however, there are no resources that concentrate on describing the regulatory role of PTMs in PPIs. We developed several methods based on residue co-evolution and proximity to predict the functional associations of pairs of PTMs that we apply to modifications in the same protein and between two interacting proteins. In order to make data available for understudied organisms, PTMcode v2 (http://ptmcode.embl.de) includes a new strategy to propagate PTMs from validated modified sites through orthologous proteins. The second release of PTMcode covers 19 eukaryotic species from which we collected more than 300,000 experimentally verified PTMs (>1,300,000 propagated) of 69 types extracting the post-translational regulation of >100,000 proteins and >100,000 interactions. In total, we report 8 million associations of PTMs regulating single proteins and over 9.4 million interplays tuning PPIs.
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