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

IFn-γ-inducing epitope prediction IFN-γ epitopes with potential to induce the release of IFN-γ from CD4+ T cells from both MEVs were predicted by "IFNepitope" server (http://crdd.osdd.net/raghava/ ifnepitope/scan.php) using the "Motif and SVM hybrid" (MERCI: Motif-EmeRging and with Classes-Identification, and SVM) approach. The tool generates overlapping sequences from the query protein/antigen and uses it for IFN-γ-inducing epitope prediction. The prediction is based on a dataset of IFN-γ-inducing and IFN-γ-noninducing MHC class II binders. 54 For both MEVs, AlgPred was used for allergenicity prediction (http://crdd.osdd.net/raghava/algpred/submission.html). 56 The AlgPred prediction of allergens is based on similarity of the known epitope with any region of the submitted protein. VaxiJen (http://www.ddg-pharmfac.net/vaxijen/ VaxiJen/VaxiJen.html) was used to analyze the probability of antigenicity of both MEVs. 57 The VaxiJen analysis applies an alignment-free approach that is solely based on the physicochemical properties of the sequences of the submitted proteins.