Predict and analyze protein glycation sites with the mRMR and IFS methods

BioMed Research International

Volumn 2015, Issue , 2015, Pages

  Liu, Yan ^a   Gu, Wenxiang ^a,b   Zhang, Wenyi ^a   Wang, Jianan ^a  

^a NORTHEAST NORMAL UNIVERSITY   (China)

^b Changchun Architecture and Civil Engineering College   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID COMPOSITION; ANALYTIC METHOD; ARTICLE; PROTEIN GLYCOSYLATION; SUPPORT VECTOR MACHINE; BIOLOGY; CHEMISTRY; GENETICS; GLYCOSYLATION; PROCEDURES; PROTEOMICS; SEQUENCE ANALYSIS;

AMINO ACID; PROTEIN;

AMINO ACIDS; COMPUTATIONAL BIOLOGY; GLYCOSYLATION; PROTEINS; PROTEOMICS; SEQUENCE ANALYSIS, PROTEIN; SUPPORT VECTOR MACHINE;

EID: 84928809810     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2015/561547     Document Type: Article

References (28)

1. X. Ling, N. Sakashita, M. Takeya, R. Nagai, S. Horiuchi, and K. Takahashi, "Immunohistochemical distribution and subcellular localization of three distinct specific molecular structures of advanced glycation end products in human tissues, " Laboratory Investigation, vol. 78, no. 12, pp. 1591-1606, 1998.
2. N. Blom, T. Sicheritz-Pontén, R. Gupta, S. Gammeltoft, and S. Brunak, "Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence, " Proteomics, vol. 4, no. 6, pp. 1633-1649, 2004.
3. K. C. Chou and C. T. Zhang, "Prediction of protein structural classes, " Critical Reviews in Biochemistry andMolecular Biology, vol. 30, no. 4, pp. 275-349, 1995.
4. G. Ji, X. Wu, Y. Shen, J. Huang, and Q. Q. Li, "A classificationbased prediction model of messenger RNA polyadenylation sites, " Journal ofTheoretical Biology, vol. 265, no. 3, pp. 287-296, 2010.
5. L. L. Hu, S. B. Wan, S. Niu et al. , "Prediction and analysis of protein palmitoylation sites, " Biochimie, vol. 93, no. 3, pp. 489-496, 2011.
6. W. Zhang, X. Xu, M. Yin, N. Luo, J. Zhang, and J. Wang, "Prediction of methylation sites using the composition of Kspaced amino acid pairs, " Protein and Peptide Letters, vol. 20, no. 8, pp. 911-917, 2013.
7. S. Li, B. Liu, R. Zeng, Y. Cai, and Y. Li, "Predicting Oglycosylation sites in mammalian proteins by using SVMs, " Computational Biology and Chemistry, vol. 30, no. 3, pp. 203-208, 2006.
8. C. Caragea, J. Sinapov, A. Silvescu, D. Dobbs, and V. Honavar, "Glycosylation site prediction using ensembles of Support Vector Machine classifiers, " BMC Bioinformatics, vol. 8, article 438, 2007.
9. Y.-Z. Chen, Y.-R. Tang, Z.-Y. Sheng, and Z. Zhang, "Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of spaced amino acid pairs, " BMC Bioinformatics, vol. 9, article 101, 2008.
10. M. B. Johansen, L. Kiemer, and S. Brunak, "Analysis and prediction of mammalian protein glycation, " Glycobiology, vol. 16, no. 9, pp. 844-853, 2006.
11. C. Zou, J. Gong, and H. Li, "An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis, " BMC Bioinformatics, vol. 14, article 90, 2013.
12. S. Kawashima, P. Pokarowski, M. Pokarowska, A. Kolinski, T. Katayama, and M. Kanehisa, "AAindex: amino acid index database, progress report 2008, " Nucleic Acids Research, vol. 36, no. 1, pp. D202-D205, 2008.
13. W. R. Atchley, J. Zhao, A. D. Fernandes, and T. Druke, "Solving the protein sequence metric problem, " Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 18, pp. 6395-6400, 2005.
14. H. Peng, F. Long, and C. Ding, "Feature selection based on mutual information: criteria of max-dependency, maxrelevance, and min-redundancy, " IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 27, no. 8, pp. 1226-1238, 2005.
15. B.-Q. Li, L.-L. Hu, S. Niu, Y.-D. Cai, and K.-C. Chou, "Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches, " Journal of Proteomics, vol. 75, no. 5, pp. 1654-1665, 2012.
16. V. N. Vapnik, TheNature of Statistical LearningTheory, Springer, New York, NY, USA, 1995.
17. T.-K. Seo, "Classification of nucleotide sequences using support vector machines, " Journal of Molecular Evolution, vol. 71, no. 4, pp. 250-267, 2010.
18. C. C. Chang and C. J. Lin, "LIBSVM: a library for support vector machines, " 2001, http://www. csie. ntu. edu. tw/?cjlin/libsvm.
19. V. Neduva, R. Linding, I. Su-Angrand et al. , "Systematic discovery of new recognition peptides mediating protein interaction networks, " PLoS Biology, vol. 3, no. 12, 2005.
20. R. Apweiler, M. J. Martin, C. O'Donovan et al. , "The universal protein resource (UniProt) in 2010, " Nucleic Acids Research, vol. 38, pp. D142-D148, 2010.
21. J. Gao, J. Wang, and M. Yin, "Experimental analyses on phase transitions in compiling satisfiability problems, " Science China Information Sciences, pp. 1-11, 2015.
22. X. Li and M. Yin, "Modified cuckoo search algorithm with self adaptive parameter method, " Information Sciences, vol. 298, pp. 80-97, 2015.
23. X. Li and M. Yin, "Modified differential evolution with selfadaptive parameters method, " Journal of Combinatorial Optimization, 2014.
24. P. Huang and M. Yin, "An upper (lower) bound forMax (MIN) CSP, " Science China Information Sciences, vol. 57, no. 7, pp. 1-9, 2014.
25. X. Li and M. Yin, "Multiobjective binary biogeography based optimization for feature selection using gene expression data, " IEEE Transactions onNanobioscience, vol. 12, no. 4, pp. 343-353, 2013.
26. X. Li and M. Yin, "An opposition-based differential evolution algorithm for permutation flow shop scheduling based on diversity measure, " Advances in Engineering Software, vol. 55, pp. 10-31, 2013.
27. X. Li and M. Yin, "Application of differential evolution algorithm on self-potential data, " PLoS ONE, vol. 7, no. 12, Article ID e51199, 2012.
28. X. Zhao, W. Zhang, X. Xu, Z. Ma, and M. Yin, "Prediction of protein phosphorylation sites by using the composition of spaced amino acid pairs, " PLoS ONE, vol. 7, no. 10, Article ID e46302, 2012.