Abstract

Dengue is causing significant morbidity and mortality worldwide. In poor and underdeveloped countries, the disease is spreading at an alarming rate due to a rise in population density and a decline in environmental cleanliness. Due to the mutation and variety of distinct dengue virus species, the disease is difficult to cure with standard techniques. In addition, there is still a need for effective vaccination against this fatal virus. Designing a vaccine needs a full explanation of the structural characteristics of the NS3 protease, the primary antigenic component of the virus. Several bioinformatics methods were utilized in this study to characterize the NS3 protease of the dengue virus utilizing data from various public databases. Different physio-chemical properties were determined using the ProtParam tool. Secondary structure and motifs were predicted using the SOPMA server and MEME suit. Finally, homology modeling of the selected protein was conducted using the PHYRE2 server. Quality assessment of the predicted structures was performed by employing Ramachandran plot, ERRAT, RAMPAGE, verify 3D, and RMSD scores to establish and suggest one best model for further experimentation. A satisfactory validation score in all those quality assessments implies the proposed model to be a good fit for the future experiment on this protein. Such homology modeling of the viral protein paves the way to a successful protein model and consequently leads to efficient vaccine design.

Keywords

Dengue 4 NS3 protease, Motif analysis, homology modeling

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