ArticleNucleic acids research2016
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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91 citing papers in PubMed.
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- Crosstalk Between Lysine Lactylation and Acetylation Regulates Lactate Dehydrogenase in Streptococcus mutans.Genomics, proteomics & bioinformatics · 2025Article
- Theoretical Investigation of the Material Usage During On-Bead Enrichment of Post-Translationally Modified Peptides in Suspension Systems.Molecules (Basel, Switzerland) · 2025Article
- Multiple regulatory mechanisms, functions and therapeutic potential of chaperone-mediated autophagy.Theranostics · 2025Review
- PPM1G and its diagnostic, prognostic and therapeutic potential in HCC (Review).International journal of oncology · 2024Review
- Importance of PTM of FLT3 in acute myeloid leukemia.Acta biochimica et biophysica Sinica · 2024Review
- A pan-respiratory antiviral chemotype targeting a transient host multi-protein complex.Open biology · 2024Article
- The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation.Nature communications · 2024Article
- The impact of genetically controlled splicing on exon inclusion and protein structure.PloS one · 2024Article
- Methyl-CpG-binding 2 K271 lactylation-mediated M2 macrophage polarization inhibits atherosclerosis.Theranostics · 2024Article
- A Pan-Respiratory Antiviral Chemotype Targeting a Host Multi-Protein Complex.bioRxiv : the preprint server for biology · 2023Article
- Characterization of Proteoform Post-Translational Modifications by Top-Down and Bottom-Up Mass Spectrometry in Conjunction with Annotations.Journal of proteome research · 2023Article
- Control of protein stability by post-translational modifications.Nature communications · 2023Review
- Evolutionary Divergence of Phosphorylation to Regulate Interactive Protein Networks in Lower and Higher Species.International journal of molecular sciences · 2022Article
- Global Profiling of 2-hydroxyisobutyrylome in Common Wheat.Genomics, proteomics & bioinformatics · 2022Article
- Current status of PTMs structural databases: applications, limitations and prospects.Amino acids · 2022Review
- Proteomic analysis of heat-stable proteins revealed an increased proportion of proteins with compositionally biased regions.Scientific reports · 2022Article
- Hornerin deposits in neuronal intranuclear inclusion disease: direct identification of proteins with compositionally biased regions in inclusions.Acta neuropathologica communications · 2022Article
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- CPLM 4.0: an updated database with rich annotations for protein lysine modifications.Nucleic acids research · 2022Article
31 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource.
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