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Computational Molecular Biology 2014, Vol. 4, No. 13, 1-6
http://cmb.biopublisher.ca
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Figure 2 model generated using 1IZLD
Figure 3model generated using 3A0B
Figure 4 model generated using3WU2
Figure 5 model generated using4IL6
1.6 Model validation
The final models were further subjected to Rampage
server for the analysis of backbone confirmation of
protein. The backbone confirmation for each models
generated which showed the number of residues lying
in allowed region, favoured region and in outlier
regions. Depending upon these characters the best
model is selected. The ANOLEA server was used to
find out Z-score and Q-mean score. Least Z-score
indicates the best model. The validated models
information and backbone confirmation is given in
Table 8 and Table 9. the backbone confirmtion of
protein models are given in Figure 6-Figure 9.
1.7 Selection of best model
However the best model is selected on the basis of
identity, query coverage, Z-score, Qmean score,
E-value etc.
2 Result
2.1 Sequence retrieval result
The sequence of PHOTOSYSTEMII D2 protein was
retrivred from uniprot with uniprotID of P06005. The
function, location, catalytic activity is given below.
Table 8 Result obtained from ANOLEA-SWISS SERVER
Templates
QMEAN score
Z-score
1IZL
0.156
-7.194
4IL6
0.314
-5.356
3A0B
0.311
-5.382
3WU2
0.366
-5.439