ArticleNucleic acids research2014
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 33 citations in OpenAlex.
- NphosNet: Predicting Protein N-Phosphorylation Sites via xLSTM and Enhanced PLM Features with a Weighted Three-Channel Cross-Attention Mechanism.Interdisciplinary sciences, computational life sciences · 2026Article
- Current status of PTMs structural databases: applications, limitations and prospects.Amino acids · 2022Review
- dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.Nucleic acids research · 2022Article
- A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra.Briefings in bioinformatics · 2021Article
- Prediction and analysis of multiple protein lysine modified sites based on conditional wasserstein generative adversarial networks.BMC bioinformatics · 2021Article
- Human carbonic anhydrases and post-translational modifications: a hidden world possibly affecting protein properties and functions.Journal of enzyme inhibition and medicinal chemistry · 2020Review
- SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites.Genomics, proteomics & bioinformatics · 2020Article
- Comparative Analysis of the Secretome and Interactome ofFrontiers in immunology · 2020Article
- dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.Nucleic acids research · 2019Article
- Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.BMC systems biology · 2017Article
- Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features.BMC bioinformatics · 2017Article
- Dynamic Lipid-dependent Modulation of Protein Topology by Post-translational Phosphorylation.The Journal of biological chemistry · 2017Article
- SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites.BMC genomics · 2016Article
- A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases.BMC systems biology · 2016Article
- dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.Nucleic acids research · 2016Article
- ASAP: a machine learning framework for local protein properties.Database : the journal of biological databases and curation · 2016Article
- dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation.Nucleic acids research · 2015Article
- A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs.BMC bioinformatics · 2015Article
- Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities.BMC bioinformatics · 2015Article
- Characterization and identification of protein O-GlcNAcylation sites with substrate specificity.BMC bioinformatics · 2014Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transmembrane (TM) proteins have crucial roles in various cellular processes. The location of post-translational modifications (PTMs) on TM proteins is associated with their functional roles in various cellular processes. Given the importance of PTMs in the functioning of TM proteins, this study developed topPTM (available online at http://topPTM.cse.yzu.edu.tw), a new dbPTM module that provides a public resource for identifying the functional PTM sites on TM proteins with structural topology. Experimentally verified TM topology data were integrated from TMPad, TOPDB, PDBTM and OPM. In addition to the PTMs obtained from dbPTM, experimentally verified PTM sites were manually extracted from research articles by text mining. In an attempt to provide a full investigation of PTM sites on TM proteins, all UniProtKB protein entries containing annotations related to membrane localization and TM topology were considered potential TM proteins. Two effective tools were then used to annotate the structural topology of the potential TM proteins. The TM topology of TM proteins is represented by graphical visualization, as well as by the PTM sites. To delineate the structural correlation between the PTM sites and TM topologies, the tertiary structure of PTM sites on TM proteins was visualized by Jmol program. Given the support of research articles by manual curation and the investigation of domain-domain interactions in Protein Data Bank, 1347 PTM substrate sites are associated with protein-protein interactions for 773 TM proteins. The database content is regularly updated on publication of new data by continuous surveys of research articles and available resources.
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