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

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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/. Proteins 2008.