Issue 2, 2015

A novel feature extraction scheme for prediction of protein–protein interaction sites

Abstract

Identifying protein–protein interaction (PPI) sites plays an important and challenging role in some topics of biology. Although many methods have been proposed, this problem is still far away to be solved. Here, a feature selection approach with an 11-sliding window and random forest algorithm is proposed, which is called DX-RF. This method has achieved an accuracy of 88.79%, recall of 82.09%, and precision of 85.76% with top-ranked 34 features on the Hetero test dataset and has 91.6% accuracy, 89.2% precision, 83.54% recall with top-ranked 25 features set on the Homo test dataset. Compared to other methods, the results indicate that the DX-RF method has a strong ability to select relevance features to get a higher performance. Moreover, in order to further understand protein interactions, feature analysis in this study is also performed.

Graphical abstract: A novel feature extraction scheme for prediction of protein–protein interaction sites

Supplementary files

Article information

Article type
Paper
Submitted
22 Oct 2014
Accepted
14 Nov 2014
First published
14 Nov 2014

Mol. BioSyst., 2015,11, 475-485

Author version available

A novel feature extraction scheme for prediction of protein–protein interaction sites

X. Du, A. Jing and X. Hu, Mol. BioSyst., 2015, 11, 475 DOI: 10.1039/C4MB00625A

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