Supersecondary structure prediction using Chou's pseudo amino acid composition

Journal of Computational Chemistry
Dongsheng ZouYuxian Xia

Abstract

Supersecondary structures (SSSs) are the building blocks of protein 3D structures. Accurate prediction of SSSs can be one important step toward building a tertiary structure from the specified secondary structure. How to improve the accuracy of prediction of SSSs by effectively incorporating the sequence order effects is an important and challenging problem. Based on a different form of Chou's pseudo amino acid composition, a novel approach for feature representation of SSSs is proposed. Amino acid basic compositions, dipeptide components, and amino acid composition distribution are incorporated to represent the compositional features of proteins. Each supersecondary structural motif is characterized as a vector of 36 dimensions. In addition, we propose a novel prediction system by using SVM and IDQD algorithm as classifiers. Our method is trained and tested on ArchDB40 dataset containing 3088 proteins. The highest overall accuracy for the training dataset and the independent testing dataset are 77.7 and 69.4%, respectively.

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Citations

Nov 2, 2011·Journal of Industrial Microbiology & Biotechnology·Wei ChenHao Lin
Jan 11, 2013·Nucleic Acids Research·Wei ChenKuo-Chen Chou
Mar 22, 2014·International Journal of Molecular Sciences·Yue-Nong FanKuo-Chen Chou
Jan 29, 2014·International Journal of Molecular Sciences·Wang-Ren QiuKuo-Chen Chou
Apr 16, 2014·Analytical Biochemistry·Wei ChenKuo-Chen Chou
Jun 14, 2013·Computational and Mathematical Methods in Medicine·Peng-Mian FengHao Lin
May 20, 2015·International Journal of Molecular Sciences·Qiaoying HuangYong Zhou
Nov 10, 2015·Journal of Theoretical Biology·Md Nasrul IslamMd Tamjidul Hoque
Aug 10, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiao Wang, Guo-Zheng Li
Jun 27, 2014·BioMed Research International·Wei ChenKuo-Chen Chou
Dec 29, 2013·BioMed Research International·Jian-Liang MinKuo-Chen Chou
Aug 27, 2014·Journal of Theoretical Biology·Jia WenStephen S T Yau
Nov 14, 2012·Journal of Theoretical Biology·Xiwu Yang, Tianming Wang
Feb 18, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Shibiao WanSun-Yuan Kung
Nov 30, 2019·Current Pharmaceutical Design·Kuo-Chen Chou
Jan 3, 2020·Molecular Genetics and Genomics : MGG·Kuo-Chen Chou
Jul 27, 2017·Computational Intelligence and Neuroscience·Xiao WangYong Gan
Dec 21, 2010·Journal of Theoretical Biology·Kuo-Chen Chou

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