Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning
Joint Authors
Ning, Qiao
Zhang, Jian
Zhao, Xiaowei
Ma, Zhiqiang
Yin, Minghao
Sun, Pingping
Source
Mathematical Problems in Engineering
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-7, 7 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-09-09
Country of Publication
Egypt
No. of Pages
7
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Zhao, Xiaowei& Zhang, Jian& Ning, Qiao& Sun, Pingping& Ma, Zhiqiang& Yin, Minghao. 2013. Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning. Mathematical Problems in Engineering،Vol. 2013, no. 2013, pp.1-7.
https://search.emarefa.net/detail/BIM-1031779
Modern Language Association (MLA)
Zhao, Xiaowei…[et al.]. Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning. Mathematical Problems in Engineering No. 2013 (2013), pp.1-7.
https://search.emarefa.net/detail/BIM-1031779
American Medical Association (AMA)
Zhao, Xiaowei& Zhang, Jian& Ning, Qiao& Sun, Pingping& Ma, Zhiqiang& Yin, Minghao. Identification of Protein Pupylation Sites Using Bi-Profile Bayes Feature Extraction and Ensemble Learning. Mathematical Problems in Engineering. 2013. Vol. 2013, no. 2013, pp.1-7.
https://search.emarefa.net/detail/BIM-1031779
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1031779