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OJBTM
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
ABSTRACT
Sarika J, Iquebal MA, Rai A., In silico analysis and homology model of legume antioxidant
proteins, Onl 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.
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