PEDS Advance Access originally published online on June 24, 2005
Protein Engineering Design and Selection 2005 18(8):365-368; doi:10.1093/protein/gzi041
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CTKPred: an SVM-based method for the prediction and classification of the cytokine superfamily
Institute of Bioinformatics and System Biology, MOE Key Laboratory of Bioinfomatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Department of Biological Science and Biotechnology, Tsinghua University, Beijing 100084, China
1 To whom correspondence should be addressed. E-mail: sunzhr{at}mail.tsinghua.edu.cn
Cell proliferation, differentiation and death are controlled by a multitude of cell–cell signals and loss of this control has devastating consequences. Prominent among these regulatory signals is the cytokine superfamily, which has crucial functions in the development, differentiation and regulation of immune cells. In this study, a support vector machine (SVM)-based method was developed for predicting families and subfamilies of cytokines using dipeptide composition. The taxonomy of the cytokine superfamily with which our method complies was described in the Cytokine Family cDNA Database (dbCFC) and the dataset used in this study for training and testing was obtained from the dbCFC and Structural Classification of Proteins (SCOP). The method classified cytokines and non-cytokines with an accuracy of 92.5% by 7-fold cross-validation. The method is further able to predict seven major classes of cytokine with an overall accuracy of 94.7%. A server for recognition and classification of cytokines based on multi-class SVMs has been set up at http://bioinfo.tsinghua.edu.cn/~huangni/CTKPred/.
Keywords: classification/dipeptide composition/cytokine/prediction/support vector machine/SVM
Received March 5, 2005; accepted May 18, 2005.
Edited by Paul Carter
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