2.3.5 ǀ Computational modeling of three-dimensional (3-D) structure of cpOAS1 protein
The three-dimensional model was generated using MODELLER 10.1 (https://salilab.org/modeller/), SWISS-MODEL (https://swissmodel.expasy.org/), PHYRE2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) and GENO3D (https://geno3d-prabi.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GENO3D/geno3d_home.html) software. In MODELLER 10.1, the 3-D structure was predicted as per the described procedure48. During this procedure, five three-dimensional structures were generated using 4 rwp as the template. The best possible structure was selected considering the DOPE (Discrete Optimized Protein Energy) score. SWISS-MODEL software was used to generate a refined 3-D model of the cpOAS1 protein. Generated cpOAS1 model was predicted sequentially with the global model quality estimate (GMQE) and the QMEAN score49. Intensive modeling mode was used to predict the 3-D structure using protein homology/analogY recognition engine V 2.0 (PHYRE2)50. In this model, the template was selected based on heuristics to maximize confidence, percentage identity and alignment coverage. In GENO3D, out of five models, the low energy model was selected for evaluation and further validation51. All 3-D structures of the cpOAS1 protein generated by all the four types of software/server were then evaluated to test the structural integrity through various online model evaluation servers included Errat52, PROCHECK53 and VERIFY3D54. Ramachandran plot as evaluated by PROCHECK was generated to check the stereochemical properties of cpOAS1 protein structure which has been modeled55. In this plot, structural validation was done by evaluating the number of amino acid residues in favoured regions, allowed regions and disallowed regions. Graphical inspections and similarity of the generated P2 model with the template model (4rwp) were done using UCSF Chimera56(http://www.cgl.ucsf.edu/chimera/). Different protein models were viewed in the RasMol.