Classification of antimicrobial peptide using diversity measure with quadratic discriminant analysis

Journal of Microbiological Methods

Volumn 78, Issue 1, 2009, Pages 94-96

  Chen, Wei ^a   Luo, Liaofu ^a  

^a INNER MONGOLIA UNIVERSITY   (China)

Author keywords

Antimicrobial peptides; Dipeptide composition; Increment of diversity; Quadratic discrimination

Indexed keywords

POLYPEPTIDE ANTIBIOTIC AGENT;

ALGORITHM; ARTICLE; BIOLOGICAL ACTIVITY; DISCRIMINANT ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS;

ALGORITHMS; ANTI-INFECTIVE AGENTS; ANTINEOPLASTIC AGENTS; ANTIVIRAL AGENTS; BACTERIOCINS; DISCRIMINANT ANALYSIS;

EID: 67349137114     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2009.03.013     Document Type: Article

References (33)

1. Bradshaw J.P. Cationic antimicrobial peptides: issues for potential clinical use. BioDrugs 17 (2003) 233-240
2. Chou K.C. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics 21 (2005) 10-19
3. Chou K.C., and Zhang C.T. Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol. 30 (1995) 275-349
4. Cole A.M., and Ganz T. Human antimicrobial peptides: analysis and application. Biotechniques 29 (2000) 822-831
5. Feng Y.E., and Luo L.F. Use of tetrapeptide signals for protein secondary-structure prediction. Amino Acids 35 (2008) 607-614
6. García-Olmedo F., Molina A., Alamillo J.M., and Rodríguez-Palenzuéla P. Plant defense peptides. Biopolymers 47 (1998) 479-491
7. Gartia A. Sur un remarquable exemple d'antagonisme entre deux souches de colibacille. Comput. Rend. Soc. Biol. 93 (1925) 1040-1041
8. Gromiha M.M., Ahmad S., and Suwa M. Application of residue distribution along the sequence for discriminating outer membrane proteins. Comput. Biol. Chem. 29 (2005) 135-142
9. Hancock R.E. Cationic peptides: effectors in innate immunity and novel antimicrobials. Lancet, Infect. Dis. 1 (2001) 156-164
10. Hancock R.E., and Lehrer R. Cationic peptides: a new source of antibiotics. Trends Biotechnol. 16 (1998) 82-88
11. Hancock R.E., and Patrzykat A. Clinical development of cationic antimicrobial peptides: from natural to novel antibiotics. Curr. Drug Targets. Infect. Disord. 2 (2002) 79-83
12. Hoffmann J.A., Reichhart J.M., and Hetru C. Innate immunity in higher insects. Curr. Opin. Immunol. 8 (1996) 8-13
13. Kamysz W., Okruèj M., and Łukasiak J. Novel properties of antimicrobial peptides. Acta Biochim. Pol. 50 (2003) 461-469
14. Kirkup Jr. B.C. Bacteriocins as oral and gastrointestinal antibiotics: theoretical considerations, applied research, and practical applications. Curr. Med. Chem. 13 (2006) 3335-3350
15. Laxton R.R. The measure of diversity. J. Theor. Biol. 70 (1978) 51-67
16. Lehrer R.I., and Ganz T. Defensins of vertebrate animals. Curr. Opin. Immunol. 14 (2002) 96-102
17. Li W.Z., Jaroszewski L., and Godzik A. Clustering of highly homologous sequences to reduce the size of large protein database. Bioinformatics 17 (2001) 282-283
18. Luo L.F., and Lv J. Sequence pattern recognition in genome analysis. Computation in Modern Science and Engineering: Proceedings of the International Conference on Computational Methods in Science and Engineering 2007 vol. 963 (2007) 1278-1281
19. Lv J., and Luo L.F. Prediction for human transcription start site using diversity measure with quadratic discrimination. Bioinformation 2 (2008) 316-321
20. Papagianni M. Ribosomally synthesized peptides with antimicrobial properties: biosynthesis, structure, function, and applications. Biotechnol. Adv. 21 (2003) 465-499
21. Rinaldi A.C. Antimicrobial peptides from amphibian skin: an expanding scenario. Curr. Opin. Chem. Biol. 6 (2002) 799-804
22. Scott M.G., and Hancock R.E. Cationic antimicrobial peptides and their multifunctional role in the immune system. Crit. Rev. Immunol. 20 (2000) 407-431
23. Snelling A.M. Effects of probiotics on the gastrointestinal tract. Curr. Opin. Infect. Dis. 18 (2005) 420-426
24. Toke O. Antimicrobial peptides: new candidates in the fight against bacterial infections. Biopolymers 80 (2005) 717-735
25. Tossi A. Host defense peptides: roles and applications. Curr. Protein Pept. Sci. 6 (2005) 1-3
26. Wang S.Q., Yang J., and Chou K.C. Using stacked generalization to predict membrane protein types based on pseudo amino acid composition. J. Theor. Biol. 242 (2006) 941-946
27. Wang G., Li X., and Wang Z. APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res. 37 (2009) D933-D937
28. Xiao X., Shao S.H., Ding Y.S., Huang Z.D., and Chou K.C. Using cellular automata images and pseudo amino acid composition to predict protein sub-cellular location. Amino Acids 30 (2006) 49-54
29. Xiao X., Shao S.H., Huang Z.D., and Chou K.C. Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor. J. Comput. Chem. 27 (2006) 478-482
30. Zhang M.Q. Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 565-568
31. Zhang L.R., and Luo L.F. Splice site prediction with quadratic discriminant analysis using diversity measure. Nucleic Acids Res. 31 (2003) 6214-6220
32. Zhang S.W., Pan Q., Zhang H.C., Shao Z.C., and Shi J.Y. Prediction protein homo-oligomer types by pseudo amino acid composition: approached with an improved feature extraction and naive Bayes feature fusion. Amino Acids 30 (2006) 461-468
33. Zhou G.P., and Cai Y.D. Predicting protease types by hybridizing gene ontology and pseudo amino acid composition. Proteins 63 (2006) 681-684