In-silico analysis predicting the best model for photosystemIID2 Protein of Spinaciaolearacea using multiple templates  

Pranati Swain
Orissa university of agriculture and technology, India
Author    Correspondence author
Computational Molecular Biology, 2014, Vol. 4, No. 13   doi: 10.5376/cmb.2014.04.0013
Received: 04 Dec., 2014    Accepted: 26 Dec., 2014    Published: 30 Dec., 2014
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Preferred citation for this article:

Swain, 2014, In-silico analysis predicting the best model for photosystemIID2 Protein of Spinaciaolearacea using multiple templates, Computational Molecular Biology, Vol.4, No.13, 1-6 (doi: 10.5376/cmb.2014.04.0013)

Abstract

Spinach is a natural medicine against diabetes, prostate cancer, asthma, constipation, high blood pressure. Spinach acts as anti-inflammatory, antiproliferative, antioxidative. In this study the PHOTOSYSTEMII D2 protein has considered for in-silico analysis. Models of the protein were generated using 1IZLD, 3A0B, 3WU2, 4IL6 templates. The sequence retrieved from uniprot, templates were predicted by usingblastP tool, physico-chemical analysis showed the properties of protein using prot-param tool , secondary structure prediction showed helices, turns and sheets using CFFSP server, homologous models were generated using modeller9.12 tool, backbone confirmation was performed by using Rampage server and finally the best model generated by using 3A0B template having 94.0% of residues lying in favored region, 2.0% residues lying in outlier region, with 91% of query coverage and 95% of identity with photosystemQ (B) protein of Thermosynechocuccus vulcanus.

Keywords
PHOTOSYSTEMII D2 protein; Template prediction; Homology modeling; Model validation; Best model prediction
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