※ Phosphorylation databases
1. HPRD release 9 : HPRD currently contains information for 16,972 PTMs which belong to various categories with phosphorylation (10,858), dephosphorylation (3,118) and glycosylation (1,860) forming the majority of the annotated PTMs. At least one enzyme responsible for PTMs has been annotated for 8,960 PTMs, which resulted in the documentation of 7,253 enzyme - substrate relationships (Keshava Prasad, et al., 2009).
2. SysPTM 2.0 : provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools (Li, et al., 2009).
3. PHOSIDA : a posttranslational modification database, comprises more than 80,000 phosphorylated, N-glycosylated or acetylated sites from nine different species. All sites are obtained from high-resolution mass spectrometric data using the same stringent quality criteria. PHOSIDA is comprised of three main components: the database environment, the prediction platform and the toolkit section (Gnad, et al., 2007; Gnad, et al., 2009; Gnad, et al., 2011).
4. PhosphoSitePlus : a new version of PhosphoSite, is a web-based database to collect protein modification sites, including protein phosphorylation sites from scientific literature as well as high-throughput discovery programs. Currently, PhosphoSitePlus contains over 120,000 phosphorylation sites
5. dbPTM : an informative resource of experimental post-translational modifications (PTMs) obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins (Lee, et al., 2006; Lu, et al., 2013).
6. UniProt :
7. PhosphoGRID : an online database of experimentally verified in vivo protein phosphorylation sites in the model eukaryotic organism S. cerevisiae. he database includes results from both high throughput (HTP) MS proteomics studies in addition to phosphosites identified in low throughput (LTP) studies of individual proteins or protein complexes (Stark, et al., 2010; Stark, et al., 2013).
8. Phospho.ELM 9.0 : contains 8,718 experimentally verified phosphorylated proteins from different species with 3,370 tyrosine, 31,754 serine and 7,449 threonine sites (Diella, et al., 2004; Diella, et al., 2008; Dinkel, et al., 2011).
9. PhosphoPep 2.0 : contains MS-derived phosphorylation data from 4 different organisms, including fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae) (Bodenmiller, et al., 2008).