Predicting lysine phosphoglycerylation with fuzzy SVM by incorporating k-spaced amino acid pairs into Chou׳s general PseAAC

Journal of Theoretical Biology
Zhe JuHong Gu

Abstract

As a new type of post-translational modification, lysine phosphoglycerylation plays a key role in regulating glycolytic process and metabolism in cells. Due to the traditional experimental methods are time-consuming and labor-intensive, it is important to develop computational methods to identify the potential phosphoglycerylation sites. However, the prediction performance of the existing phosphoglycerylation site predictor is not satisfactory. In this study, a novel predictor named CKSAAP_PhoglySite is developed to predict phosphoglycerylation sites by using composition of k-spaced amino acid pairs and fuzzy support vector machine. On the one hand, after many aspects of assessments, we find the composition of k-spaced amino acid pairs is more suitable for representing the protein sequence around the phosphoglycerylation sites than other encoding schemes. On the other hand, the proposed fuzzy support vector machine algorithm can effectively handle the imbalanced and noisy problem in phosphoglycerylation sites training dataset. Experimental results indicate that CKSAAP_PhoglySite outperforms the existing phosphoglycerylation site predictor Phogly-PseAAC significantly. A matlab software package for CKSAAP_PhoglySite can be freely...Continue Reading

References

Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Feb 5, 2008·IEEE Transactions on Neural Networks·Chun-Fu Lin, Sheng-De Wang
Dec 21, 2010·Journal of Theoretical Biology·Kuo-Chen Chou
Jan 11, 2013·Nucleic Acids Research·Wei ChenKuo-Chen Chou
Feb 22, 2013·Bioinformatics·Dong-Sheng CaoYi-Zeng Liang
Mar 29, 2013·Molecular BioSystems·Kuo-Chen Chou
Aug 3, 2013·Science·Raymond E Moellering, Benjamin F Cravatt
Nov 12, 2013·Nucleic Acids Research·Zexian LiuYu Xue
Apr 10, 2014·Molecular Systems Biology·Sylvain LanouetteJean-François Couture

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Citations

Sep 1, 2016·BioMed Research International·Ming Jiang, Jun-Zhe Cao
Sep 6, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Xuanguo NanZhiqiang Ma
Oct 28, 2019·Current Topics in Medicinal Chemistry·Kuo-Chen Chou
Nov 30, 2019·Current Pharmaceutical Design·Kuo-Chen Chou
Nov 30, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Tao LiCangzhi Jia
Jan 3, 2020·Molecular Genetics and Genomics : MGG·Kuo-Chen Chou
Dec 6, 2019·Database : the Journal of Biological Databases and Curation·Lei ZhengYongchun Zuo
Jan 10, 2021·Genes·Abel Avitesh ChandraTatushiko Tsunoda
Jun 19, 2017·Molecular Therapy. Nucleic Acids·Bin LiuKuo-Chen Chou

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