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Author:

Xu, W.-L. (Xu, W.-L..) | Li, A. (Li, A..) (Scholars:李昂) | Wang, M.-H. (Wang, M.-H..) | Jiang, Z.-H. (Jiang, Z.-H..) | Feng, H.-Q. (Feng, H.-Q..)

Indexed by:

Scopus PKU CSCD

Abstract:

In this work a novel method was proposed to predict the relative solvent accessibilities of residues from protein primary sequences. This method was based on support vector regression (SVR) and used the local information of the particular residue for prediction as input. Three data sets, RS-126, Manesh-215 and CB-513, were collected and used to evaluate prediction performance. With 3-fold cross validation test, the average of mean absolute error (MAE) and correlation coefficient (CC) for different data set were consistently better than a previous method called RVP-Net which was based on a multilayer feed-forward neural network. In addition, we used multiple sequence alignment as input information and obtained a prediction result of 16.8% for MAE and 0.562 for CC, which was superior to that obtained with single sequence input. The results demonstrate the efficiency of this method and that the support vector regression is a useful tool for proteomics prediction analysis.

Keyword:

Bioinformatics; Machine learning; Protein structure prediction; Relative solvent accessibility; Support vector machine

Author Community:

  • [ 1 ] [Xu, W.-L.]Department of Electronic Science and Technology, University of Science and Technology of China, Hefei 230026, China
  • [ 2 ] [Li, A.]Department of Electronic Science and Technology, University of Science and Technology of China, Hefei 230026, China
  • [ 3 ] [Wang, M.-H.]College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
  • [ 4 ] [Jiang, Z.-H.]Department of Electronic Science and Technology, University of Science and Technology of China, Hefei 230026, China
  • [ 5 ] [Feng, H.-Q.]Department of Electronic Science and Technology, University of Science and Technology of China, Hefei 230026, China

Reprint Author's Address:

  • [Xu, W.-L.]Department of Electronic Science and Technology, University of Science and Technology of China, Hefei 230026, China

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Source :

Chinese Journal of Biomedical Engineering

ISSN: 0258-8021

Year: 2007

Issue: 1

Volume: 26

Page: 1-5

Cited Count:

WoS CC Cited Count:

SCOPUS Cited Count:

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 7

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