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Online Journal of Bioinformatics©
Volume 13(1):120-129, 2012.
In silico analysis and homology model of legume antioxidant proteins.
Sarika J1, Iquebal MA2 and Rai A1
1Centre for Agricultural Bioinformatics, 2Division of Biometrics and Statistical Modelling, Indian Agricultural Statistics Research Institute, PUSA, New Delhi, INDIA
Sarika J, Iquebal MA, Rai A., In silico analysis and homology model of legume antioxidant proteins, Online J Bioinform, 13(1):120-129, 2012. The availability of plant genome data has stimulated in silico homology modelling of plant proteins which are structurally unknown. The conserved domain database search analysis to determine domain and motif showed that the antioxidants were found to belong to Cu-Zu Superoxide-Dismutase super family. In this study physico-chemical and functional characterization of antioxidant proteins in chickpea, rajmash, pea and vigna were determined. Self-optimized prediction with alignment was used to calculate the secondary structural features of protein sequences. The 3-D structure was determined by GENO3D and SWISS-MODEL. SWISS-MODEL proved to be more precise using SAVS. Stereochemical properties and quality of the modelled structures were then assessed by Ramchandran plot analysis validated with PROCHECK. The modelled structures could be used as a foundation for functional analysis of experimentally derived crystal structures.
Keywords: Antioxidants, Chickpea, Homology modelling, Ramachandran plot, Swiss-Model