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Proteins. 2008 Feb 1;70(2):404-14.

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

Author information

1
Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China.

Abstract

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 http://bioinfo.au.tsinghua.edu.cn/phoscan/.

PMID:
17680694
DOI:
10.1002/prot.21563
[Indexed for MEDLINE]

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