ReviewPloS one2013
Systematic analysis and prediction of pupylation sites in prokaryotic proteins.
Review in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed, 28 citations in OpenAlex.
- Mapping the structural heterogeneity of Pup ligase PafA using H/D exchange mass spectrometry.The Journal of biological chemistry · 2025Article
- Identifying Pupylation Proteins and Sites by Incorporating Multiple Methods.Frontiers in endocrinology · 2022Article
- PUP-Fuse: Prediction of Protein Pupylation Sites by Integrating Multiple Sequence Representations.International journal of molecular sciences · 2021Article
- PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids.Genes · 2020Article
- Peptides containing the PCNA interacting motif APIM bind to the β-clamp and inhibit bacterial growth and mutagenesis.Nucleic acids research · 2020Article
- RF-MaloSite and DL-Malosite: Methods based on random forest and deep learning to identify malonylation sites.Computational and structural biotechnology journal · 2020Article
- Recognition of Protein Pupylation Sites by Adopting Resampling Approach.Molecules (Basel, Switzerland) · 2018Article
- CIPPN: computational identification of protein pupylation sites by using neural network.Oncotarget · 2017Article
- EPuL: An Enhanced Positive-Unlabeled Learning Algorithm for the Prediction of Pupylation Sites.Molecules (Basel, Switzerland) · 2017Article
- Positive-Unlabeled Learning for Pupylation Sites Prediction.BioMed research international · 2016Article
- The Absence of Pupylation (Prokaryotic Ubiquitin-Like Protein Modification) Affects Morphological and Physiological Differentiation in Streptomyces coelicolor.Journal of bacteriology · 2015Article
- Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.PloS one · 2015Article
- Prokaryotic ubiquitin-like protein modification.Annual review of microbiology · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prokaryotic ubiquitin-like protein (Pup) is the first identified prokaryotic protein that is functionally analogous to ubiquitin. Recent studies have shed light on the Pup activation and conjugation to target proteins to be a signal for the selective degradation proteins in Mycobacterium tuberculosis (Mtb). By covalently conjugating the Pup, pupylation functions as a critical post-translational modification (PTM) conserved in actinomycetes. Detecting pupylation sites is crucial and fundamental for understanding the molecular mechanisms of Pup. Yet comparative studies with other PTM suggest that the development of accurate and complete repertories of pupylation is still in its early stages. Unbiased screening for pupylation sites by experimental methods is time consuming and expensive; in silico prediction can provide highly potential candidates and reduce the number of potential candidates that require further in vivo or in vitro confirmation. Here, we present an effective classifier of PupPred for predicting pupylation sites, which shows better performance than existing classifiers. Importantly, this work not only investigates the sequential, structural and evolutionary hallmarks around pupylation sites but also compares the differences of pupylation and ubiquitylation from the environmental, conservative and functional characterization of substrates. These prediction and analysis results may be helpful for further experimental investigation of degradation proteins in prokaryotes. Finally, the PupPred server is available at http://bioinfo.ncu.edu.cn/PupPred.aspx.
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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 OpenQuestion graph.