Paper Citing NAMD - Abstract
Jain, Amisha; Tripathi, Pranav; Shrotriya, Aniket; Chaudhary, Ritu; Singh, Ajeet
In silico analysis and modeling of putative T cell epitopes for vaccine design of Toscana virus
3 BIOTECH, 5:497-503, AUG 2015
The sandfly fever Toscana virus is an important etiological agent known to cause human neurological infections in endemic Mediterranean countries during summer season. In the present study, prediction and modeling of T cell epitopes of Toscana virus (TOSV) antigenic proteins followed by the binding simulation studies of predicted highest binding scorers with their corresponding MHC class II alleles were done. Immunoinformatics was applied in computational vaccinology to analyze the viral proteins which generate possible outcomes to elicit vaccine for TOSV. Here, immunoinformatic tool ProPred was used to predict the promiscuous MHC class II epitopes of viral antigenic proteins. The molecular modeling of the selected epitopes as well as MHC alleles was done at CPH model 3.2 server. Molecular dynamics (MD) simulation studies were performed through the NAMD graphical user interface embedded in visual molecular dynamics. The epitope/peptide VKMMIVLNL of viral nucleoprotein as well as VMILGLLSS of viral glycoprotein has shown the highest binding score with the same DRB1*1104 MHC II allele. These two predicted peptides are highly potential to induce T cell-mediated immune response and are expected to be useful in designing epitope-based vaccines after further testing. The results signify that the nucleoprotein, glycoprotein or the combination of both could be useful for future development of a vaccine controlling the spread of this emerging virus that could pose a new threat for humans.
