KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W588-94. doi: 10.1093/nar/gkm322. Epub 2007 May 21.


Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. Herein, a new web server, KinasePhos 2.0, incorporates support vector machines (SVM) with the protein sequence profile and protein coupling pattern, which is a novel feature used for identifying phosphorylation sites. The coupling pattern [XdZ] denotes the amino acid coupling-pattern of amino acid types X and Z that are separated by d amino acids. The differences or quotients of coupling strength C(XdZ) between the positive set of phosphorylation sites and the background set of whole protein sequences from Swiss-Prot are computed to determine the number of coupling patterns for training SVM models. After the evaluation based on k-fold cross-validation and Jackknife cross-validation, the average predictive accuracy of phosphorylated serine, threonine, tyrosine and histidine are 90, 93, 88 and 93%, respectively. KinasePhos 2.0 performs better than other tools previously developed. The proposed web server is freely available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • Computational Biology / methods*
  • Computer Simulation
  • Internet
  • Markov Chains
  • Neural Networks, Computer
  • Phosphoproteins / chemistry*
  • Phosphoproteins / metabolism
  • Phosphorylation
  • Probability
  • Protein Kinases / metabolism*
  • Sensitivity and Specificity
  • Sequence Analysis, Protein / methods*
  • Software*
  • User-Computer Interface


  • Phosphoproteins
  • Protein Kinases