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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, Lucknow 226014, India

 

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.


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