Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach

Proteins. 2008 Feb 1;70(2):404-14. doi: 10.1002/prot.21563.


Protein phosphorylation plays important roles in a variety of cellular processes. Detecting possible phosphorylation sites and their corresponding protein kinases is crucial for studying the function of many proteins. This article presents a new prediction system, called PhoScan, to predict phosphorylation sites in a kinase-family-specific way. Common phosphorylation features and kinase-specific features are extracted from substrate sequences of different protein kinases based on the analysis of published experiments, and a scoring system is developed for evaluating the possibility that a peptide can be phosphorylated by the protein kinase at the specific site in its sequence context. PhoScan can achieve a specificity of above 90% with sensitivity around 90% at kinase-family level on the data experimented. The system is applied on a set of human proteins collected from Swiss-Prot and sets of putative phosphorylation sites are predicted for protein kinase A, cyclin-dependent kinase, and casein kinase 2 families. PhoScan is available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Odds Ratio
  • Phosphorylation
  • Protein Kinases / metabolism*
  • Substrate Specificity


  • Protein Kinases