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Extracting Physicochemical Features to Predict Protein Secondary Structure
Joint Authors
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-8, 8 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-05-14
Country of Publication
Egypt
No. of Pages
8
Main Subjects
Medicine
Information Technology and Computer Science
Abstract EN
We propose a protein secondary structure prediction method based on position-specific scoring matrix (PSSM) profiles and four physicochemical features including conformation parameters, net charges, hydrophobic, and side chain mass.
First, the SVM with the optimal window size and the optimal parameters of the kernel function is found.
Then, we train the SVM using the PSSM profiles generated from PSI-BLAST and the physicochemical features extracted from the CB513 data set.
Finally, we use the filter to refine the predicted results from the trained SVM.
For all the performance measures of our method, Q3 reaches 79.52, SOV94 reaches 86.10, and SOV99 reaches 74.60; all the measures are higher than those of the SVMpsi method and the SVMfreq method.
This validates that considering these physicochemical features in predicting protein secondary structure would exhibit better performances.
American Psychological Association (APA)
Huang, Yin-Fu& Chen, Shu-Ying. 2013. Extracting Physicochemical Features to Predict Protein Secondary Structure. The Scientific World Journal،Vol. 2013, no. 2013, pp.1-8.
https://search.emarefa.net/detail/BIM-1032800
Modern Language Association (MLA)
Huang, Yin-Fu& Chen, Shu-Ying. Extracting Physicochemical Features to Predict Protein Secondary Structure. The Scientific World Journal No. 2013 (2013), pp.1-8.
https://search.emarefa.net/detail/BIM-1032800
American Medical Association (AMA)
Huang, Yin-Fu& Chen, Shu-Ying. Extracting Physicochemical Features to Predict Protein Secondary Structure. The Scientific World Journal. 2013. Vol. 2013, no. 2013, pp.1-8.
https://search.emarefa.net/detail/BIM-1032800
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1032800