Hello so the current research question is given in the topic. The study is essentially a proteomics based study of the ns2b/ns3 protease of the DENV-2 strain and seeing how that protease is common in other members of the flaviviridae family. The hypothesis is listed below. The softwares you would be required to use to answer this research question would primarily be BLAST(for analysis of phylogenetic trees), COBALT and Swiss PDB viewer.
Hypothesis It has been experimentally proven that phenolic compounds such as trans-ferulic acid n from extracts of the Carica papaya leaf have an effect on inhibiting the growth of the NS2B-NS3 protease receptor in the DENV-2. This prevents the replication of the viral strain (Ghosh & Talukdar, 265). The NS2B-NS3 protease receptor is a key factor in viral replication and evading innate immunity. Due to the fact that the protease receptor structure is present in different serotypes of the DENV strain, it may be present in other viral strains of the Flaviviridae family. If structural similarities are present between the NS2B-NS3 protease receptor protein in DENV and another strain in the Flaviviridae family, it could potentially mean that trans-ferulic acid from the Carica papaya leaf could prove to exhibit anti-viral properties against that strain. This could potentially mean that ferulic acid, present in the Carica papaya leaf could affect multiple viral assemblies in the Flaviviridae family if they contain the ns2b-ns3 receptor, which would have structural similarities with the ns2b-ns3 receptor in the DENV-2 strain. The similarities between the NS2B-NS3 and the other Non-Structural proteins from other viruses such as the Zika Virus will be helpful in determining the effect of the Carica Papaya leaf extract effectiveness on the inhibition of the viral protein diverging the research aspect from DENV to other viruses of the same family.