Showing Publication Results for :

PDBSite
Full Name of the Resource : Phosphorylation sites identified by mass spectrometry
Resource Category : Databases -> Protein Sequence Databases -> Protein sequence motifs and active sites

  1. Title of the Paper : PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites (View at PubMed)
    Contributors : Gnad, F.; Ren, S.; Cox, J.; Olsen, J. V.; Macek, B.; Oroshi, M.; Mann, M.
    Address : Department for Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz, D-82152 Martinsried, Germany. gnad@biochem.mpg.de
    Publication Name : Genome Biol
    Volume : 8
    Issue : 11
    Pages : R250
    Publication Year : 2007
    ISSN : 1465-6914 (Electronic) 1465-6906 (Linking)
    Language : English
    Abstract : PHOSIDA http://www.phosida.com, a phosphorylation site database, integrates thousands of high-confidence in vivo phosphosites identified by mass spectrometry-based proteomics in various species. For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites.



  2. Title of the Paper : Phospho.ELM: a database of phosphorylation sites--update 2011 (View at PubMed)
    Contributors : Dinkel, H.; Chica, C.; Via, A.; Gould, C. M.; Jensen, L. J.; Gibson, T. J.; Diella, F.
    Address : SCB Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
    Publication Name : Nucleic Acids Res
    Volume : 39
    Issue : Database issue
    Pages : D261-7
    Publication Year : 2011
    ISSN : 1362-4962 (Electronic) 0305-1048 (Linking)
    Language : English
    Abstract : The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42,574 serine, threonine and tyrosine non-redundant phosphorylation sites. Several new features have been implemented, such as structural disorder/order and accessibility information and a conservation score. Additionally, the conservation of the phosphosites can now be visualized directly on the multiple sequence alignment used for the score calculation. Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases.