1. Prediction of protein–protein interactions based on PseAA composition and hybrid feature selection
- Author
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Liu, Liang, Cai, Yudong, Lu, Wencong, Feng, Kaiyan, Peng, Chunrong, and Niu, Bing
- Subjects
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PROTEIN-protein interactions , *AMINO acid analysis , *BIOINFORMATICS , *PROTEOMICS , *PREDICTION models , *COMPUTER algorithms , *NEAREST neighbor analysis (Statistics) - Abstract
Abstract: Based on pseudo amino acid (PseAA) composition and a novel hybrid feature selection frame, this paper presents a computational system to predict the PPIs (protein–protein interactions) using 8796 protein pairs. These pairs are coded by PseAA composition, resulting in 114 features. A hybrid feature selection system, mRMR–KNNs–wrapper, is applied to obtain an optimized feature set by excluding poor-performed and/or redundant features, resulting in 103 remaining features. Using the optimized 103-feature subset, a prediction model is trained and tested in the k-nearest neighbors (KNNs) learning system. This prediction model achieves an overall accurate prediction rate of 76.18%, evaluated by 10-fold cross-validation test, which is 1.46% higher than using the initial 114 features and is 6.51% higher than the 20 features, coded by amino acid compositions. The PPIs predictor, developed for this research, is available for public use at http://chemdata.shu.edu.cn/ppi. [Copyright &y& Elsevier]
- Published
- 2009
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