Sequence and structure-based prediction of eukaryotic protein phosphorylation sites

J Mol Biol. 1999 Dec 17;294(5):1351-62. doi: 10.1006/jmbi.1999.3310.


Protein phosphorylation at serine, threonine or tyrosine residues affects a multitude of cellular signaling processes. How is specificity in substrate recognition and phosphorylation by protein kinases achieved? Here, we present an artificial neural network method that predicts phosphorylation sites in independent sequences with a sensitivity in the range from 69 % to 96 %. As an example, we predict novel phosphorylation sites in the p300/CBP protein that may regulate interaction with transcription factors and histone acetyltransferase activity. In addition, serine and threonine residues in p300/CBP that can be modified by O-linked glycosylation with N-acetylglucosamine are identified. Glycosylation may prevent phosphorylation at these sites, a mechanism named yin-yang regulation. The prediction server is available on the Internet at via e-mail to NetPhos@cbs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Consensus Sequence*
  • Eukaryotic Cells / chemistry*
  • Glycosylation
  • Models, Molecular
  • Neural Networks, Computer
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / metabolism
  • Phosphoproteins / chemistry*
  • Phosphoproteins / metabolism*
  • Phosphorylation
  • Phylogeny
  • Protein Structure, Tertiary
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Serine / metabolism
  • Substrate Specificity
  • Threonine / metabolism
  • Trans-Activators / chemistry
  • Trans-Activators / metabolism
  • Tyrosine / metabolism


  • Nuclear Proteins
  • Phosphoproteins
  • Trans-Activators
  • Threonine
  • Tyrosine
  • Serine