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Computational Molecular Biology 2014, Vol. 4, No. 13, 1-6
http://cmb.biopublisher.ca
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2.2Physico-chemical analysis result
From this analysis the amino acid composition,
theoretical PI, number of positively and negatively
charged residues, GRAVY, aliphatic index of the
protein is found.
2.3 Selected templates
Four primer 1IZL, 4IL6, 3A0B, 3WU2 were selected
after blastP run as the templates for the protein with
following characters. Here more templates are
selected in order to find out best model for protein
with a suitable template.
2.4 Secondary structure prediction result
The secondary structure of protein which generated
from CFFSP server showed the following result.
2.5 Homology modelling result
The finally generated models were visualised using
PyMol visualiser. The helices were denoted with sky
blue colurs and the loops were denoted with purple
colours respectively. The atom count, formal charge
sum, molecular surface area, solvent accessible
surface area of the models were generated from PyMol
and beta factor, stability of the models, VDW radius,
minimized enegy were generated fromYasara tool.
2.6 Model validation analysis result
The finally generated models were submitted to
Rampage server to find out the best protein. The best
protein was predicted on the basis of residues lying in
strong favoured region.
3 Discussions
From the above analysis the best model found for
photosystemII D2 protein with the template 3A0B
having 94.0% of residues lying in favoured region,
2.0% residues lying in outlier region, with 91% of
query coverage and 95% of identity with
photosystemQ (B) protein of Thermosynechocuccus
vulcanus.
References
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