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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.