Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM

Computational and Mathematical Methods in Medicine
Yunyun LiangShengli Zhang

Abstract

Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM). Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS), segmented PsePSSM, and segmented autocovariance transformation (ACT) based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640) are adopted in this paper. Then a 700-dimensional (700D) feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA). To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to oth...Continue Reading

References

Jun 17, 1976·Nature·M Levitt, C Chothia
Dec 20, 1987·Journal of Molecular Biology·L Patthy
Jul 20, 1973·Science·C B Anfinsen
Jan 1, 1995·Critical Reviews in Biochemistry and Molecular Biology·K C Chou, C T Zhang
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 13, 1999·Journal of Protein Chemistry·G P Zhou
Oct 21, 1999·Biochemical and Biophysical Research Communications·K C Chou
Mar 1, 2002·Computers & Chemistry·Yu-Dong CaiKuo-Chen Chou
Aug 30, 2002·European Journal of Biochemistry·Rui-yan LuoJia-kun Liu
Sep 11, 2004·Biochemical and Biophysical Research Communications·Kuo-Chen Chou, Yu-Dong Cai
Jul 19, 2005·Biochemical and Biophysical Research Communications·Hong-Bin ShenKuo-Chen Chou
Jan 18, 2006·BMC Bioinformatics·Youfang CaoKexuan Tang
Aug 16, 2006·Journal of Theoretical Biology·Chao ChenJin-Yuan Mo
Aug 19, 2007·Analytical Biochemistry·Kuo-Chen Chou, Hong-Bin Shen
Nov 13, 2007·Protein Engineering, Design & Selection : PEDS·Hong-Bin Shen, Kuo-Chen Chou
Jan 5, 2010·Peptides·Lezheng YuYuhong Zeng
Jul 13, 2011·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·Robert L BarryJohn C Gore
Jun 23, 2012·PloS One·Xia-Yu XiaXian-Ming Pan
Mar 13, 2014·Journal of Theoretical Biology·Shuyan DingYuhua Yao

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Methods Mentioned

BETA
feature extraction
PCA

Software Mentioned

SegPseP
ACT
- BLAST )
LIBSVM
AADP
BLAST
SegACP
LCC
PSSM AC
MBMGAC

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