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.