4.1.1 Homology modelling and structure-based functional
prediction of Rv2615c protein
The sequence of Rv2615c protein was retrieved from Mycobrowser and
subjected to various servers for structure and function-based
predictions. Antigenicity of Rv2615c was estimated in Vaxijen 2.0 server
with a set threshold default value of 0.4 (Doytchinova and Flower,
2007).
The secondary structure and the structure-based function of Rv2615c
protein was predicted using I-TASSER (Iterative Threading ASSEmbly
Refinement) server. Structural analogs, Gene ontology (GO) template
analogs and consensus GO terms for biological process and molecular
functions were predicted (Roy, Kucukural and Zhang, 2010). Five
homology-based models were predicted for Rv2615c. Chiron server was used
for energy minimization of models (Ramachandran et al. , 2011).
The output models were validated for their stereo-chemical quality
through PROCHECK, VERIFY3D and ERRAT server (Lüthy, Bowie and Eisenberg,
1992; Laskowski et al. , 1996). PROCHECK confirms the quality of
protein structure by Ramachandran plot where <5 residues in
the disallowed region are considered to constitute a good structure. The
best model of protein structure was selected with fewer residues in
disallowed region of Ramachandran plot, high score in VERIFY3D and
ERRAT.