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P3DB specifications

Information


Unique identifier OMICS_03237
Name P3DB
Alternative name Plant Protein Phosphorylation DataBase
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Dong Xu

Publication for Plant Protein Phosphorylation DataBase

P3DB citations

 (16)
library_books

iPTMnet: an integrated resource for protein post translational modification network discovery

2017
Nucleic Acids Res
PMCID: 5753337
PMID: 29145615
DOI: 10.1093/nar/gkx1104

[…] idence source for low-throughput experiments. For example, for TIF5A in maize (http://research.bioinformatics.udel.edu/iptmnet/entry/P80639/#asSub), the phosphorylation information for S2 and S4 from P3DB source is from a large-scale paper ‘Large-scale analysis of phosphorylated proteins in maize leaf’ (), while RLIMS-P provides additional support for Ser2 phosphorylation from a low-throughput exp […]

library_books

Proteomic Analysis Reveals Key Proteins and Phosphoproteins upon Seed Germination of Wheat (Triticum aestivum L.)

2015
Front Plant Sci
PMCID: 4649031
PMID: 26635843
DOI: 10.3389/fpls.2015.01017

[…] (Cline et al., ). According the sequences of certain phosphoproteins, the occurring of homologous protein phosphorylation in different species was searched in Plant Protein Phosphorylation Data Base (P3DB, http://www.p3db.org/index.php). Prediction of phosphorylated modification sites was done in NetPhos (version 2.0, http://www.cbs.dtu.dk/services/NetPhos/) (Blom et al., ) based on protein sequen […]

library_books

Multiplex staining of 2 DE gels for an initial phosphoproteome analysis of germinating seeds and early grown seedlings from a non orthodox specie: Quercus ilex L. subsp. ballota [Desf.] Samp.

2015
Front Plant Sci
PMCID: 4531236
PMID: 26322061
DOI: 10.3389/fpls.2015.00620

[…] ified phosphoprotein sequences downloaded from UniprotKB, NCBI nr or available in Quercus_DB (Romero-Rodriguez et al., ) were subjected to BLAST analysis by using the phosphoprotein BLAST tool in the Plant Protein Phosphorylation DataBase (P3DB) (Gao et al., ) available at http://www.p3db.org/, to find orthologous proteins whose phosphorylation sites were described previously in other species. Pro […]

library_books

Non specific lipid transfer proteins in maize

2014
BMC Plant Biol
PMCID: 4226865
PMID: 25348423
DOI: 10.1186/s12870-014-0281-8

[…] no charge. Three prediction tools, PredGPI [], big-PI Plant Predictor [] and GPI-SOM [] were used to determine the presence of GPI-anchor sites. Phosphorylation sites of the nsLTPs were predicted by P3DB (http://www.p3db.org/). A sequence identity matrix of the mature nsLTP sequences was computed using BioEdit v7.0.9.0 (http://www.mbio.ncsu.edu/bioedit/bioedit.html), which enable us to determine […]

library_books

Integrating phosphoproteomics in systems biology

2014
Comput Struct Biotechnol J
PMCID: 4204398
PMID: 25349677
DOI: 10.1016/j.csbj.2014.07.003

[…] also contain phosphorylation information for many proteins, such as HPRD and UniProt , while databases for some specific organisms have also been developed, like PhosPhat for Arabidopsis thaliana , P3DB for six plants species and phosphoPep for Drosophila . Many post-translational modification (PTM) databases include phosphosite information since it is the most common PTM; examples are Phosida […]

library_books

Quantitative phosphoproteomic profiling of fiber differentiation and initiation in a fiberless mutant of cotton

2014
BMC Genomics
PMCID: 4070576
PMID: 24923550
DOI: 10.1186/1471-2164-15-466

[…] osites were identified using Motif-X. To compare potential consensus sequences among different plant species, all phosphopeptides from our study, as well as phosphopeptides from nine other species in P3DB, were used for motif extraction against a background database generated by combining 15,070 random protein sequences derived from the genomes of the 10 species (Additional file : Table S8, sheet […]

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P3DB institution(s)
Department of Computer Science, Department of Biochemistry and CS Bond Life Sciences Center, University of Missouri, Columbia, MO, USA

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