Gpos-mploc: A top-down approach to improve the quality of predicting subcellular localization of gram-positive bacterial proteins

Protein and Peptide Letters

Volumn 16, Issue 12, 2009, Pages 1478-1484

  Shen, Hong Bin ^a,b   Chou, Kuo Chen ^a,b  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b GORDON LIFE SCIENCE INSTITUTE   (United States)

Author keywords

Homology search, representative proteins, gene ontology, functional domain, sequential evolution, ensemble classifier, fusion approach; Multiplex protein

Indexed keywords

BACTERIAL PROTEIN;

ARTICLE; BIOLOGY; CELL FRACTIONATION; GENETIC DATABASE; GRAM POSITIVE BACTERIUM; METABOLISM; METHODOLOGY; PROTEIN DATABASE;

BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; GRAM-POSITIVE BACTERIA; SUBCELLULAR FRACTIONS;

BACTERIA (MICROORGANISMS); POSIBACTERIA;

EID: 73549106100     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986609789839322     Document Type: Article

References (53)

1. Shen, H. B.; Chou, K. C. Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins. Protein Eng. Design Select., 2007, 20, 39-46.
2. Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G. Gene ontology: tool for the unification of biology. Nat. Genet., 2000, 25, 25-29.
3. Chou, K. C. Prediction of protein cellular attributes using pseudo amino acid composition. Proteins Struct. Funct.. Genet. (Erratum: ibid., 2001, Vol. 44, 60),
4. 2001, 43, 246-255.
5. Camon, E.; Magrane, M.; Barrell, D.; Binns, D.; Fleischmann, W.; Kersey, P.; Mulder, N.; Oinn, T.; Maslen, J.; Cox, A.; Apweiler, R. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res., 2003, 13, 662-672.
6. Barrell, D.; Dimmer, E.; Huntley, R. P.; Binns, D.; O'Donovan, C.; Apweiler, R. The GOA database in 2009-an integrated Gene Ontology Annotation resource. Nucleic Acids Res., 2009, 37, D396-403.
7. Chou, K. C.; Shen, H. B. Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms. Nat. Protoc., 2008, 3, 153-162.
8. Chou, K. C. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics, 2005, 21, 10-19.
9. Chen, C.; Chen, L.; Zou, X.; Cai, P. Prediction of protein secondary structure content by using the concept of Chou's pseudo amino acid composition and support vector machine. Protein Pept. Lett., 2009, 16, 27-31.
10. Ding, Y. S.; Zhang, T. L. Using Chou's pseudo amino acid composition to predict subcellular localization of apoptosis proteins: an approach with immune genetic algorithm-based ensemble classifier. Pattern Recog. Lett., 2008, 29, 1887-1892.
11. Ding, H.; Luo, L.; Lin, H. Prediction of cell wall lytic enzymes using Chou's amphiphilic pseudo amino acid composition. Protein Pept. Lett., 2009, 16, 351-355.
12. Georgiou, D. N.; Karakasidis, T. E.; Nieto, J. J.; Torres, A. Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition. J. Theor. Biol., 2009, 257, 17-26.
13. Jiang, X.; Wei, R.; Zhang, T. L.; Gu, Q. Using the concept of Chou's pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy. Protein Pept. Lett., 2008, 15, 392-396.
14. Li, F. M.; Li, Q. Z. Predicting protein subcellular location using Chou's pseudo amino acid composition and improved hybrid approach. Protein Pept. Lett., 2008, 15, 612-616.
15. Lin, H. The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition. J. Theor. Biol., 2008, 252, 350-356.
16. Lin, H.; Ding, H.; Feng-Biao Guo, F. B.; Zhang, A. Y.; Huang, J. Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition. Protein Pept. Lett., 2008, 15, 739-744.
17. Qiu, J. D.; Huang, J. H.; Liang, R. P.; Lu, X. Q. Prediction of G-protein-coupled receptor classes based on the concept of Chou's pseudo amino acid composition: an approach from discrete wavelet transform. Anal. Biochem., 2009, 390, 68-73.
18. Zeng, Y. H.; Guo, Y. Z.; Xiao, R. Q.; Yang, L.; Yu, L. Z.; Li, M. L. Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. J. Theor. Biol., 2009, 259, 366-372.
19. Zhang, G. Y.; Fang, B. S. Predicting the cofactors of oxidoreductases based on amino acid composition distribution and Chou's amphiphilic pseudo amino acid composition. J. Theor. Biol., 2008, 253, 310-315.
20. Zhang, G. Y.; Li, H. C.; Fang, B. S. Predicting lipase types by improved Chou's pseudo-amino acid composition. Protein Pept. Lett., 2008, 15, 1132-1137.
21. Zhou, X. B.; Chen, C.; Li, Z. C.; Zou, X. Y. Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes. J. Theor. Biol., 2007, 248, 546-551.
22. Ding, Y. S.; Zhang, T. L.; Chou, K. C. Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network. Protein Pept. Lett., 2007, 14, 811-815.
23. Mundra, P.; Kumar, M.; Kumar, K. K.; Jayaraman, V. K.; Kulkarni, B. D. Using pseudo amino acid composition to predict protein subnuclear localization: Approached with PSSM. Pattern Recog. Lett., 2007, 28, 1610-1615.
24. Chen, Y. L.; Li, Q. Z. Prediction of apoptosis protein subcellular location using improved hybrid approach and pseudo amino acid composition. J. Theor. Biol., 2007, 248, 377-381.
25. Zhang, T. L.; Ding, Y. S.; Chou, K. C. Prediction protein structural classes with pseudo amino acid composition: approximate entropy and hydrophobicity pattern. J. Theor. Biol., 2008, 250, 186-193.
26. Xiao, X.; Wang, P.; Chou, K. C. Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image. J. Theor. Biol., 2008, 254, 691-696.
27. Lin, H.; Li, Q. Z. Predicting conotoxin superfamily and family by using pseudo amino acid composition and modified Mahalanobis discriminant. Biochem. Biophys. Res. Commun., 2007, 354, 548-551.
28. Lin, H.; Li, Q. Z. Using Pseudo Amino Acid Composition to Predict Protein Structural Class: Approached by Incorporating 400 Dipeptide Components. J. Comput. Chem., 2007, 28, 1463-1466.
29. Xiao, X.; Lin, W. Z.; Chou, K. C. Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes. J. Comput. Chem., 2008, 29, 2018-2024.
30. Xiao, X.; Wang, P.; Chou, K. C. Predicting protein quaternary structural attribute by hybridizing functional domain composition and pseudo amino acid composition. J. Appl. Cryst., 2009, 42, 169-173.
31. Smith, C. Subcellular targeting of proteins and drugs http://www.biocompare.com/Articles/TechnologySpotlight/976/Su bcellular-Targeting-Of-Proteins-And-Drugs.html, 2008.
32. Glory, E.; Murphy, R. F. Automated subcellular location determination and high-throughput microscopy. Dev. Cell, 2007, 12, 7-16.
33. Shen, H. B.; Chou, K. C. Hum-mPLoc: An ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites. Biochem. Biophys. Res. Commun., 2007, 355, 1006-1011.
34. Chou, K. C.; Shen, H. B. Euk-mPLoc: a fusion classifier for largescale eukaryotic protein subcellular location prediction by incorporating multiple sites. J. Proteome Res., 2007, 6, 1728-1734.
35. Schaffer, A. A.; Aravind, L.; Madden, T. L.; Shavirin, S.; Spouge, J. L.; Wolf, Y. I.; Koonin, E. V.; Altschul, S. F. Improving the accuracy of PSI-BLAST protein database searches with compositionbased statistics and other refinements. Nucleic Acids Res., 2001, 29, 2994-3005.
36. Loewenstein, Y.; Raimondo, D.; Redfern, O. C.; Watson, J.; Frishman, D.; Linial, M.; Orengo, C.; Thornton, J.; Tramontano, A. Protein function annotation by homology-based inference. Genome Biol., 2009, 10, 207.
37. Gerstein, M.; Thornton, J. M. Sequences and topology Curr. Opin. Struct. Biol., 2003, 13, 341-343.
38. Chou, K. C. Review: Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134.
39. Tatusov, R. L.; Fedorova, N. D.; Jackson, J. D.; Jacobs, A. R.; Kiryutin, B.; Koonin, E. V.; Krylov, D. M.; Mazumder, R.; Mekhedov, S. L.; Nikolskaya, A. N.; Rao, B. S.; Smirnov, S.; Sverdlov, A. V.; Vasudevan, S.; Wolf, Y. I.; Yin, J. J.; Natale, D. A. The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 2003, 4, 41.
40. Finn, R. D.; Mistry, J.; Schuster-Bockler, B.; Griffiths-Jones, S.; Hollich, V.; Lassmann, T.; Moxon, S.; Marshall, M.; Khanna, A.; Durbin, R.; Eddy, S. R.; Sonnhammer, E. L.; Bateman, A. Pfam: clans, web tools and services. Nucleic Acids Res., 2006, 34, D247-251.
41. Letunic, I.; Copley, R. R.; Pils, B.; Pinkert, S.; Schultz, J.; Bork, P. SMART 5: domains in the context of genomes and networks. Nucleic Acids Res., 2006, 34, D257-260.
42. Marchler-Bauer, A.; Anderson, J. B.; Derbyshire, M. K.; DeWeese-Scott, C.; Gonzales, N. R.; Gwadz, M.; Hao, L.; He, S.; Hurwitz, D. I.; Jackson, J. D.; Ke, Z.; Krylov, D.; Lanczycki, C. J.; Liebert, C. A.; Liu, C.; Lu, F.; Lu, S.; Marchler, G. H.; Mullokandov, M.; Song, J. S.; Thanki, N.; Yamashita, R. A.; Yin, J. J.; Zhang, D.; Bryant, S. H. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res., 2007, 35, D237-240.
43. Chou, K. C.; Shen, H. B. Large-scale plant protein subcellular location prediction. J. Cell. Biochem.., 2007, 100, 665-678.
44. Gonzalez-Diaz, H.; Gonzalez-Diaz, Y.; Santana, L.; Ubeira, F. M.; Uriarte, E. Proteomics, networks, and connectivity indices. Proteomics, 2008, 8, 750-778.
45. Chou, K. C.; Shen, H. B. Review: Recent progresses in protein subcellular location prediction. Anal. Biochem., 2007, 370, 1-16.
46. Denoeux, T. A k-nearest neighbor classification rule based on Dempster-Shafer theory. IEEE Trans. Syst. Man. Cybern., 1995, 25., 804-813.
47. Chou, K. C.; Shen, H. B. Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers. J. Proteome Res., 2006, 5, 1888-1897.
48. Shen, H. B.; Chou, K. C. QuatIdent: A web server for identifying protein quaternary structural attribute by fusing functional domain and sequential evolution information. J. Proteome Res., 2009, 8, 1577-1584.
49. Chou, K. C.; Zhang, C. T. Review: Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol., 1995, 30, 275-349.
50. Chen, K.; Kurgan, L. A.; Ruan, J. Prediction of protein structural class using novel evolutionary collocation-based sequence representation. J. Comput. Chem., 2008, 29, 1596-1604.
51. Chou, K. C.; Shen, H. B. FoldRate: A web-server for predicting protein folding rates from primary sequence. Open Bioinformatics J., 2009, 3, 31-50 (openly accessible at http://www.bentham.org/open/tobioij/).
52. Shen, H. B.; Song, J. N.; Chou, K. C. Prediction of protein folding rates from primary sequence by fusing multiple sequential features. J. Biomed. Sci. Eng. (JBiSE), 2009, 2, 136-143 (openly accessible at http://www.srpublishing.org/journal/jbise/).
53. Chou, K. C.; Shen, H. B. Review: recent advances in developing web-servers for predicting protein attributes. Nat. Science, 2009, 2, 63-92 (openly accessible at http://www.scirp.org/journal/NS/).