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OJBTM
Online Journal of Bioinformatics ©
Volume
10 (1):60-66, 2009
Prediction of 3-dimensional
structure of ORF3 protein of genotype 1 hepatitis E virus
Rathi B, Naik S, Sarangi AN, Aggarwal R
Biomedical Informatics Centre, Sanjay
Gandhi Postgraduate Institute of Medical Sciences,
ABSTRACT
Rathi B, Naik S, Sarangi AN, Aggarwal R., Prediction of 3-dimensional structure of ORF3
protein of genotype 1 hepatitis E virus, Online J Bioinformatics
10(1):60-66,2009. Hepatitis E virus (HEV) is an
important human pathogen in the developing world. In the absence of an in
vitro culture system for this virus, information on its basic biology is
limited. The HEV genome consists of a linear, single-stranded, nearly 7.5 Kb
long, positive sense RNA. It contains three
overlapping open reading frames in three different coding frames. Each of the
three viral protein may represent a potential target
for host immune response. HEV pORF3, smallest of the three HEV proteins, is a
cytoskeleton-associated phosphoprotein which appears
to play a role in viral replication. Detailed structure of this protein is not
known. We therefore developed a 3-dimensional model for the HEV ORF3 protein
using MODELLER program based on a homology modeling method. Validation of the
predicted protein structure was done using DOPE, PROCHECK and WHATIF programs.
The model may provide valuable aid in designing of an inhibitor for pORF3 .
Keywords: Hepatitis E Virus, pORF3, homology
modeling, MODELLER, predictive model, DOPE, PROCHECK, WHATIF.