P3DB 3.0: From plant phosphorylation sites to protein networks

In the past few years, the Plant Protein Phosphorylation Database ((PDB)-D-3, http://p3db.org) has become one of the most significant in vivo data resources for studying plant phosphoproteomics. We have substantially updated (PDB)-D-3 with respect to format, new datasets and analytic tools. In the (PDB)-D-3 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, (PDB)-D-3 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 (PDB)-D-3 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 (PDB)-D-3 a comprehensive, systematic and interactive platform for phosphoproteomics research.