SUPPORT VECTOR MACHINE (SVM) BASED PREDICTION OF PROMISCUOUS MHC CLASS BINDING PEPTIDES

Gomase V.S.¹*, Chitlange N.R.^2
1School of Technology, S.R.T.M. University, Sub-Centre, Latur, 413531, MS, India
²School of Technology, S.R.T.M. University, Sub-Centre, Latur, 413531, MS, India
* Corresponding Author : gomase.viren@gmail.com

Received : -     Accepted : -     Published : 15-06-2010
Volume : 1     Issue : 1       Pages : 4 - 8
Int J Comput Biol 1.1 (2010):4-8

Keywords : antigen protein, epitope, PSSM, SVM, MHC, peptide vaccine
Conflict of Interest : None declared

Shigella flexneri is a species of Gram-negative bacteria in the genus Shigella that can cause diarrhea in humans. Peptide fragments of antigen protein can be used to select nonamers for use in rational vaccine design and to increase the understanding of roles of the immune system in infectious diseases. Analysis shows MHC class II binding peptides of antigen protein from Shigella flexneri are important determinant for protection of host form parasitic infection. In this assay, we used PSSM and SVM algorithms for antigen design and predicted the binding affinity of antigen protein having 574 amino acids, which shows 566 nonamers. Binding ability prediction of antigen peptides to major histocompatibility complex (MHC) class I & II molecules is important in vaccine development from Shigella flexneri.

[1] Ryan K.J., Ray C.G. (editors) (2004) Sherris Medical Microbiology (4th ed. ed.). McGraw Hill. ISBN 0- 8385-8529-9.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[2] Joshi J. Tang, Kuzma M., Wagner J., Mookerjee B., Filicko J., Carabasi M., Flomenberg N., Flomenberg P. (2009) J. Gen Virol., 90(Pt 1), 84-94.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[3] McDonald D., Stockwin L., Matzow T., Blair Zajdel M.E., Blair G.E. (1999) Gene Ther., 6(9),1512-9.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[4] Gomase V.S., Kale K.V. and Shyamkumar K. (2008) J. of Proteomics & Bioinformatics, 1 (4), 188- 205  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[5] Gomase V.S., Kale K.V., Chikhale N.J., Changbhale S.S. (2007) Curr. Drug Discov. Technol., 4(2),117-1215.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[6] Gomase V.S., Kale K.V. (2008) Int. J. of Applied Computing, 1(1), 39-46.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[7] Gomase V.S., Kale K.V. (2008) Int. J. of Applied Computing, 1(1), 33- 38.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[8] Gomase V.S., Kale K.V. (2008) Int. J. of Information Retrieval, 1(1), 11- 15.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[9] Gomase V.S., Kale K.V., Shyamkumar K., Shankar S. (2008) ICETET 2008, IEEE Computer Society in IEEE Xplore, Los Alamitos, California, 629-634  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[10] Gomase V.S., Tandale J.P., Patil S.A., Kale K.V. (2006) 14th International Conference on Advance Computing & Communication, Published by IEEE Computer Society in IEEE Xplore USA 614-615  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[11] Reche P.A., Glutting J.P., Reinherz E.L. (2002) Hum Immun., 63, 701- 709.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[12] Buus S., et al. (2003) Tissue Antigens, 62, 378-384.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[13] Nielsen M., et al. (2003) Protein Sci., 12, 1007-1017  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus