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Kinase-Specific Prediction of Protein Phosphorylation Sites

  • Martin L. Miller
  • Nikolaj Blom
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 527)

Summary

As extensive mass spectrometry-based mapping of the phosphoproteome progresses, computational anal ysis of phosphorylation-dependent signaling becomes increasingly important. The linear sequence motifs that surround phosphorylated residues have successfully been used to characterize kinase–substrate spe cificity. Here, we briefly describe the available resources for predicting kinase-specific phosphorylation from sequence properties. We address the strengths and weaknesses of these resources, which are based on methods ranging from simple consensus patterns to more advanced machine-learning algorithms. Furthermore, a protocol for the use of the artificial neural network based predictors, NetPhos and NetPhosK, is provided. Finally, we point to possible developments with the intention of providing the community with improved and additional phosphorylation predictors for large-scale modeling of cellular signaling networks.

Key words

Bioinformatics Prediction Phosphorylation Kinase Linear motifs NetPhos NetPhosK Artificial neural networks 

Notes

Acknowledgments

The authors would like to thank Rune Linding, Lars Juhl Jensen, Majbritt Hjerrild, Steen Gammeltoft, Thomas Sicheritz-Ponten and Søren Brunak.

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Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Martin L. Miller
    • 1
  • Nikolaj Blom
    • 1
  1. 1.Technical University of Denmark, Center for Biological Sequence AnalysisLyngbyDenmark

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