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Computational Molecular Biology 2014, Vol. 4, No. 15, 1-5
http://cmb.biopublisher.ca
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1.5 Model validation and optimization
Expasy server provides many online tools with the
help of which the generated protein models can be
evaluated and validated (Rambabu et al., 2012). The
generated models were then validated by using Errat,
Verify3d, Procheck saves server. The backbone
confirmation of the protein was studied by using
procheck saves server from where the residues lying
in favoured region, allowed region and outlier regions
can be found. When more residues found in favoured
region and less residues found in outlier region, then it
represents that protein is stable for further study
(Table 3). Then the final Z-score of the models were
obtained from prosa server, which showed the overall
model quality (Table 4b). The models were then
submitted to Anolea server which gave the QMEAN
score and Z-score (Table 4a).
Table 3 The backbone confirmation of models found from
rampage serve
Analysis
Protein structure Domain structure
Number of residues in
favoured region
517 ( 91.8%)
159 (88.3%)
Number of residues in
allowed region
34 (6.0%)
15 (8.3%)
Number of residues in
outlier region
12 (2.1%)
6 ( 3.3%)
Table 4 Model validation result
A Result found from anolea server
Analysis
protein
Domain
QMEAN score
0.452
0.628
Z-score
-3.206
-1.483
B Result found from prosa server
Analysis
protein
Domain
Z-score
-8.32
-4.21
1.6 Active site prediction
The active site or binding site is the region where the
ligand binds to receptor. In this study the active site
was predicted by using castp server. The active sites of
both enzyme and domain are shown in Figure 4 and
Figure 5. The active sites show the region where the
ligand can bind or not. The binding energy dependent
upon the type of residue to which it is binding i.e.,
hydrophobic or hydrophilic or polar or no-polar etc.
the residues found at active sites are given in Figure 6
and Figure 7 respectively.
1.7 Protein-ligand interaction
The interaction of ligand (FAD) was checked with
whole enzyme and only with the domain parts
separately to find out the regions where the lignad
binds properly. The interaction was studied by using
autodock tool (Jasim et al., 2013, Seeliger et al., 2010).
The pdb files of both enzyme, domain, ligand were
uploaded one after another by setting the docking
Figure 4 Binding site of whole enzyme
Figure 5 Binding site of domain