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|Alternative name||Plant Protein Phosphorylation DataBase|
|Restrictions to use||None|
- person_outline Dong Xu
Publication for Plant Protein Phosphorylation DataBase
iPTMnet: an integrated resource for protein post translational modification network discovery
[…] 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 […]
Proteomic Analysis Reveals Key Proteins and Phosphoproteins upon Seed Germination of Wheat (Triticum aestivum L.)
[…] (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 […]
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.
[…] 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 […]
Non specific lipid transfer proteins in maize
[…] 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 v18.104.22.168 (http://www.mbio.ncsu.edu/bioedit/bioedit.html), which enable us to determine […]
Integrating phosphoproteomics in systems biology
[…] 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 […]
Quantitative phosphoproteomic profiling of fiber differentiation and initiation in a fiberless mutant of cotton
[…] 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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