Protein remote homology detection by combining pseudo Dimer composition with an ensemble learning method

Current Proteomics

Volumn 13, Issue 2, 2016, Pages 86-91

  Liu, Bin ^a   Chen, Junjie ^a   Wang, Shanyi ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

Ensemble learning; Protein remote homology detection; Pseudo Dimer composition

Indexed keywords

AMINO ACID; DIMER; DIPEPTIDE; PROTEIN;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; LEARNING; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN REMOTE HOMOLOGY DETECTION; PSEUDO DIMER COMPOSITION; SEQUENCE HOMOLOGY;

EID: 84973601429     PISSN: 15701646     EISSN: None     Source Type: Journal    
DOI: 10.2174/157016461302160514002939     Document Type: Article

References (35)

1. Yeh, J.-H. and Chen, C.-H. In Protein remote homology detection based on latent topic vector model, Networking and Information Technology (ICNIT), 2010 International Conference on, IEEE: 2010, pp 456-460.
2. Liu, B.; Chen, J. and Wang, X. Protein remote homology detection by combining Chou's distance-pair pseudo amino acid composition and principal component analysis. Mol. Genetics Genomics, 2015, 290(5), 1-13.
3. Rost, B. and Rost, B. Twilight zone of protein sequence alignments. Protein Eng. 12, 85-94. Protein Eng., 1999, 12(2), 85-94.
4. Chou, K.-C. Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11(16), 2105-2134.
5. Needleman, S. B. and Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol Biol, 1970, 48(3), 443-453.
6. Smith, T. F. and Waterman, M. S. Identification of common molecular subsequences. J. Mol. Biol., 1981, 147(1), 195-197.
7. Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W. and Lipman, D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res., 1997, 25(17), 3389-3402.
8. Pearson, W. R. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics, 1991, 11(3), 635-650.
9. Eddy, S. R. Profile hidden Markov models. Bioinformatics, 1998, 14(9), 755-763.
10. Saigo, H.; Vert, J.-P.; Ueda, N. and Akutsu, T. Protein homology detection using string alignment kernels. Bioinformatics, 2004, 20(11), 1682-1689.
11. Dong, Q.-W.; Wang, X.-L. and Lin, L. Application of latent semantic analysis to protein remote homology detection. Bioinformatics, 2006, 22(3), 285-290.
12. Liu, B.; Zhang, D.; Xu, R.; Xu, J.; Wang, X.; Chen, Q.; Dong, Q. and Chou, K.-C. Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. Bioinformatics, 2014, 30(4), 472-479.
13. Liu, B. and Wang, X. Using Chou's Pseudo Amino Acid Composition for Protein Remote Homology Detection. Engineering, 2013, 5(10), 149.
14. Rangwala, H. and Karypis, G. Profile-based direct kernels for remote homology detection and fold recognition. Bioinformatics, 2005, 21(23), 4239-4247.
15. Kuang, R.; Ie, E.; Wang, K.; Wang, K.; Siddiqi, M.; Freund, Y. and Leslie, C. Profile-based string kernels for remote homology detection and motif extraction. J. Bio inform. Computat. Biol., 2005, 5(3), 527-550.
16. Liu, X.; Zhao, L. and Dong, Q. Protein remote homology detection based on auto-cross covariance transformation. Comp. Biol. Med., 2011, 41(8), 640-647.
17. Liu, B.; Wang, X.; Zou, Q.; Dong, Q. and Chen, Q. Protein Remote Homology Detection by Combining Chou's Pseudo Amino Acid Composition and Profile Based Protein Representation. Mol. Inform., 2013, 32, 775-782.
18. Ma, J.; Wang, S.; Wang, Z. and Xu, J. MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. Res. Computat. Mol. Biol., 2014, 8594, 173-174.
19. Chou, K. C. Prediction of protein cellular attributes using pseudoamino acid composition. Proteins: Structure, Function, Bioinformatics, 2001, 45(3), 246-255.
20. Liao, L. and Noble, W. Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J. Computat. Biol., 2003, 10(6), 857-868.
21. Chandonia, J. M.; Hon, G.; Walker, N. S.; Conte, L. L.; Koehl, P.; Levitt, M. and Brenner, S. E. The ASTRAL compendium in 2004. Nucleic Acids Res., 2004, 32(suppl 1), D189-D192.
22. Liu, B.; Wang, X.; Xu, R. and Tang, B. Protein Remote Homology Detection by Combining Profile-based Protein Representation with Local Alignment Kernel. J. Med. Bioeng., 2014, 5(1), 17-22.
23. Lin, C.; Chen, W. Q.; Qiu, C.; Wu, Y. F.; Krishnan, S. and Zou, Q. LibD3C: Ensemble classifiers with a clustering and dynamic selection strategy. Neurocomputing, 2014, 123, 424-435
24. Wei, L. Y.; Liao, M. H.; Gao, Y.; Ji, R. R.; He, Z. Y. and Zou, Q. Improved and Promising Identification of Human MicroRNAs by Incorporating a High-Quality Negative Set. Ieee-Acm Trans Computat.BioI. Bioinform., 2014, 11(1), 192-201.
25. Shen, H.-B. and Chou, K.-C. Ensemble classifier for protein fold pattern recognition. Bioinformatics, 2006, 22(14), 1717-1722.
26. Chou, K.-C. and Shen, H.-B. Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization. Biochem. Biophys. Res. Commun., 2006, 347(1), 150-157.
27. Lee, C. Predicting protein mutant energetics by self-consistent ensemble optimization. J. Mol. Biol., 1994, 236(3), 918-939.
28. Liu, B.; Xu, J.; Zou, Q.; Xu, R.; Wang, X. and Chen, Q. Using distances between Top-n-gram and residue pairs for protein remote homology detection. BMC Bioinformatics, 2014, 15(Suppl 2), S3.
29. Leslie, C. S.; Eskin, E.; Cohen, A.; Weston, J. and Noble, W. S. Mismatch string kernels for discriminative protein classification. Bioinformatics, 2004, 20(4), 467-476.
30. Liao, L. and Noble, W. S. Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J. Computat. Biol., 2003, 10(6), 857-868.
31. Li, L. and Noble, W. S. Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J. Computat. Biol., 2003, 10(6), 857-868.
32. Yang, Y.; Tantoso, E. and Li, K.-B. Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties. J. Theor. Biol., 2008, 252(1), 145-154.
33. Lingner, T. and Meinicke, P. Remote homology detection based on oligomer distances. Bioinformatics, 2006, 22(18), 2224-2231.
34. Lingner, T. and Meinicke, P. Word correlation matrices for protein sequence analysis and remote homology detection. BMC Bioinform., 2008, 9(1), 259.
35. Dong, Q.; Lin, L. and Wang, X. Protein remote homology detection based on binary profiles. In Bioinform. Res. Develop., Springer: 2007; pp 212-223.