Structural basis of development of multi-epitope vaccine against Middle East respiratory syndrome using in silico approach

Srivastava, Sukrit; Kamthania, Mohit; Singh, Soni; Saxena, Ajay K; Sharma, Nishi

The structural accuracy of initial model including joining of the gaps was performed by ModRefiner refinment. Galaxy-Refine was used to further refine the 3D models of CTL and HTL MEVs. For both MEVs, refined model 1 was chosen on the basis of best scorings. For CTL MEV refinement, the score of model 1 was as follows: Rama favored was 94.2%, GDT-HA was 0.9500, RMSD was 0.433, MolProbity was 2.211, Clash score was 18.3, and Poor rotamers was 1.2. For HTL MEV refinement, the score of model 1 was as follows: Rama favored was 93.4%, GDT-HA was 0.9502, RMSD was 0.412, MolProbity was 2.262, Clash score was 21.9, and Poor rotamers was 0.6. Here, MolProbity is the log-weighted combination of clash score, percentage Ramachandran not favored, and percentage bad side-chain rotamers. After refinement, all the mentioned parameters improved significantly as compared to those of the initial model (Table S10 ).