ArticleNucleic acids research2014
P³DB 3.0: From plant phosphorylation sites to protein networks.
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 31 papers.
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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.
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Who cites it
31 citing papers in PubMed, 82 citations in OpenAlex.
- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
- EPSD 2.0: An Updated Database of Protein Phosphorylation Sites Across Eukaryotic Species.Genomics, proteomics & bioinformatics · 2025Article
- Multimodal knowledge expansion widget powered by plant protein phosphorylation database and ChatGPT.Frontiers in bioinformatics · 2025Article
- Confronting the data deluge: How artificial intelligence can be used in the study of plant stress.Computational and structural biotechnology journal · 2024Review
- DecodingPlants (Basel, Switzerland) · 2024Article
- A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction.Genomics, proteomics & bioinformatics · 2023Review
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
- qPTMplants: an integrative database of quantitative post-translational modifications in plants.Nucleic acids research · 2022Article
- Regulation of PaRBOH1-mediated ROS production in Norway spruce by CaFrontiers in plant science · 2022Article
- Comparative Phosphoproteomic Analysis Reveals the Response of Starch Metabolism to High-Temperature Stress in Rice Endosperm.International journal of molecular sciences · 2021Article
- Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars.Biomolecules · 2021Article
- Comparative phosphoproteomic analysis of BR-defective mutant reveals a key role of GhSK13 in regulating cotton fiber development.Science China. Life sciences · 2020Article
- RESTful API for iPTMnet: a resource for protein post-translational modification network discovery.Database : the journal of biological databases and curation · 2020Article
- Evolution of protein kinase substrate recognition at the active site.PLoS biology · 2019Article
- Conserved phosphorylation hotspots in eukaryotic protein domain families.Nature communications · 2019Article
- Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools.International journal of molecular sciences · 2018Review
- Molecular characterization of Brassica napus stress related transcription factors, BnMYB44 and BnVIP1, selected based on comparative analysis of Arabidopsis thaliana and Eutrema salsugineum transcriptomes.Molecular biology reports · 2018Article
- Peroxiredoxins and Redox Signaling in Plants.Antioxidants & redox signaling · 2018Review
- iPTMnet: an integrated resource for protein post-translational modification network discovery.Nucleic acids research · 2018Article
- Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics.Frontiers in plant science · 2018Review
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
In the past few years, the Plant Protein Phosphorylation Database (P(3)DB, http://p3db.org) has become one of the most significant in vivo data resources for studying plant phosphoproteomics. We have substantially updated P(3)DB with respect to format, new datasets and analytic tools. In the P(3)DB 3.0, there are altogether 47 923 phosphosites in 16 477 phosphoproteins curated across nine plant organisms from 32 studies, which have met our multiple quality standards for acquisition of in vivo phosphorylation site data. Centralized by these phosphorylation data, multiple related data and annotations are provided, including protein-protein interaction (PPI), gene ontology, protein tertiary structures, orthologous sequences, kinase/phosphatase classification and Kinase Client Assay (KiC Assay) data--all of which provides context for the phosphorylation event. In addition, P(3)DB 3.0 incorporates multiple network viewers for the above features, such as PPI network, kinase-substrate network, phosphatase-substrate network, and domain co-occurrence network to help study phosphorylation from a systems point of view. Furthermore, the new P(3)DB reflects a community-based design through which users can share datasets and automate data depository processes for publication purposes. Each of these new features supports the goal of making P(3)DB a comprehensive, systematic and interactive platform for phosphoproteomics research.
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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.