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Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning

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  • Xiaowei Zhao
  • Jian Zhang
  • Qiao Ning
  • Pingping Sun
  • Zhiqiang Ma
  • Minghao Yin

Abstract

Pupylation, one of the most important posttranslational modifications of proteins, typically takes place when prokaryotic ubiquitin-like protein (Pup) is attached to specific lysine residues on a target protein. Identification of pupylation substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of pupylation. Comparing with the labor-intensive and time-consuming experiment approaches, computational prediction of pupylation sites is much desirable for their convenience and fast speed. In this study, a new bioinformatics tool named EnsemblePup was developed that used an ensemble of support vector machine classifiers to predict pupylation sites. The highlight of EnsemblePup was to utilize the Bi-profile Bayes feature extraction as the encoding scheme. The performance of EnsemblePup was measured with a sensitivity of 79.49%, a specificity of 82.35%, an accuracy of 85.43%, and a Matthews correlation coefficient of 0.617 using the 5-fold cross validation on the training dataset. When compared with other existing methods on a benchmark dataset, the EnsemblePup provided better predictive performance, with a sensitivity of 80.00%, a specificity of 83.33%, an accuracy of 82.00%, and a Matthews correlation coefficient of 0.629. The experimental results suggested that EnsemblePup presented here might be useful to identify and annotate potential pupylation sites in proteins of interest. A web server for predicting pupylation sites was developed.

Suggested Citation

  • Xiaowei Zhao & Jian Zhang & Qiao Ning & Pingping Sun & Zhiqiang Ma & Minghao Yin, 2013. "Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning," Mathematical Problems in Engineering, Hindawi, vol. 2013, pages 1-7, September.
  • Handle: RePEc:hin:jnlmpe:283129
    DOI: 10.1155/2013/283129
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