MAIN


©1996-2013  All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the  before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or  re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.


OJBTM

 Online Journal of Bioinformatics © 

 Volume 14 (1): 9-14, 2013


In silico prediction and conservancy analysis of promiscuous epitopes in a novel adenovirus HAdV-65

 

Rezaul Islam MD1, Lamia Khan1, Amran Gazi MD1, Motaher Hossain1, Farhana Shafrin2, Aubhishek Zaman3, Ahsan Habib Polash2

 

1Department of Biochemistry and Molecular Biology, 2Molecular Biology Laboratory, 3Department of Genetic Engineering and Biotechnology, University of Dhaka, Bangladesh.


ABSTRACT

 

Islam R, Khan L, Gazi A, Hossain M, Shafrin F, Zaman A, Polash AH., In silico prediction and conservancy analysis of promiscuous epitopes in a novel adenovirus HAdV-65, Online J Bioinform., 14 (1):9-14, 2013. Human adenovirus-65 has been associated with infantile gastroenteritis in Bangladesh. In Silico promiscuous epitopes for antigenic capsid proteins and core components of HAdV-65 followed by conservancy analysis in 3 randomly selected genotypes 1, 2 and 3 from NCBI database from different regions were determined.  A total of 191,056 candidate promiscuous epitopes for MHC-I molecules based on their binding affinity to different MHC-I alleles were predicted. Epitopes having an IC50 score ≤ 50 nM were selected from TAP, proteasomal, IC50 scores, and number of interactions with epitopes interacting with ≥ 3 MHC-I alleles. From this data, a catalogue of epitopes was created.  Hexon protein had most (26.14%), T cell promiscuous epitopes of all the viral antigenic proteins. A total of 219 T cell epitopes were predicted to be promiscuous binders against 51 MHC-II alleles and 23 epitopes were predicted to bind with all of the subjected MHC-II alleles. A considerable number of predicted epitopes having higher affinity for both MHC-I and MHC-II alleles were found to be conserved in other adenovirus genotypes and may be potential candidates for design of epitope vaccines. To our knowledge, this study is the first in silico method to predict promiscuous epitopes for antigenic proteins in HAdV-65 and must be validated by In-vitro tests. 

 

Keywords: Adenovirus; in silico; epitope based vaccine; promiscuous T cell epitopes


MAIN

 

FULL-TEXT(SUBSCRIBERS)