3.3.5 ǀ Computational modeling of three-dimensional (3-D) structure of cpOAS1 protein
The best possible 3-D structure of cpOAS1 obtained from MODELLER 9.18, SWISS-MODEL, PHYRE 2 and GENO3D were designated as P1, P2, P3, P4, respectively (FIGURE7). These models were evaluated and their results are shown in Table 9. Based on Errat, PROCHECK and VERIFY3D validations, the model generated by SWISS-MODEL was found to be the best model for the prediction of cpOAS1 protein structure. The overall quality of model P2 determined by ERRAT value (96.35%) and VERIFY3D score (92.81%) was the highest and the stereo-chemical properties checked by PROCHECK were found to be the best among all the four models (Table 9). Model P2 along with its Ramachandran Plot (FIGURE 8) showed that there were 94.6 % residues in the most favoured region and 5.4 % additional allowed regions (%) and none in the disallowed region. Further, in the P2 model, global model quality estimation (GMQE) and qualitative model energy analysis (QMEAN) values were 0.86 and 0.26, respectively, which are in the acceptable range. In the P2 model, the GMQE score reflects the expected accuracy of that alignment and is expressed as a number between 0 and 1 where higher numbers indicate higher reliability. The QMEAN is a composite scoring function describing the major geometrical aspects of protein structures. Result of the superimposition of the P2 model and porcine (4rwp) generated in UCSF Chimera and the ProSA-web web server indicated that the P2 model was almost similar in structure (FIGURE 8B). The Z-score of the P2 model was found to be -8.32 which was within the range of porcine OAS protein (-10.09), the best template (4rwp; FIGURE 10S).