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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, 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
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