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Open AccessCommunication

Predicting Apoptosis Protein Subcellular Locations based on the Protein Overlapping Property Matrix and Tri-Gram Encoding

by Yang Yang 1,†, Huiwen Zheng 2,†, Chunhua Wang 3,†, Wanyue Xiao 1 and Taigang Liu 3,4,*
1
AIEN Institute, Shanghai Ocean University, Shanghai 201306, China
2
College of Sciences & Engineering, University of Tasmania, 7001 Tasmania, Australia
3
College of Information Technology, Shanghai Ocean University, Shanghai 201306, China
4
Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai 201306, China
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2019, 20(9), 2344; https://doi.org/10.3390/ijms20092344
Received: 1 April 2019 / Revised: 25 April 2019 / Accepted: 8 May 2019 / Published: 11 May 2019
(This article belongs to the Special Issue Artificial Intelligence and Computer Aided Drug Design)
To reveal the working pattern of programmed cell death, knowledge of the subcellular location of apoptosis proteins is essential. Besides the costly and time-consuming method of experimental determination, research into computational locating schemes, focusing mainly on the innovation of representation techniques on protein sequences and the selection of classification algorithms, has become popular in recent decades. In this study, a novel tri-gram encoding model is proposed, which is based on using the protein overlapping property matrix (POPM) for predicting apoptosis protein subcellular location. Next, a 1000-dimensional feature vector is built to represent a protein. Finally, with the help of support vector machine-recursive feature elimination (SVM-RFE), we select the optimal features and put them into a support vector machine (SVM) classifier for predictions. The results of jackknife tests on two benchmark datasets demonstrate that our proposed method can achieve satisfactory prediction performance level with less computing capacity required and could work as a promising tool to predict the subcellular locations of apoptosis proteins. View Full-Text
Keywords: tri-gram; protein overlapping property matrix; subcellular location; support vector machine; recursive feature elimination tri-gram; protein overlapping property matrix; subcellular location; support vector machine; recursive feature elimination
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MDPI and ACS Style

Yang, Y.; Zheng, H.; Wang, C.; Xiao, W.; Liu, T. Predicting Apoptosis Protein Subcellular Locations based on the Protein Overlapping Property Matrix and Tri-Gram Encoding. Int. J. Mol. Sci. 2019, 20, 2344.

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