Blog 1

Dr. Deng and I are researching how drugs inhibit the HIV virus using molecular dynamic. This study will help and guide researchers in the drug discovery industry to better understand how such drugs work. This will help researchers design and create a better drug to treat HIV-AIDS virus. So far this summer I learned what molecular dynamics is and how it is used. I also learned how molecular dynamics became successful and what some of the challenges are. Molecular dynamics provides an atomistic insights about the structure and dynamics of proteins and nucleic acids.
The first Molecular dynamic simulation actually furthered our knowledge about proteins because it revealed the dynamic nature of a folded protein. I was able to apply my Biology 101 knowledge to the simulation once I saw the protein folding. Furthermore, I learned how a drug molecule finds its target binding site. Molecular dynamics actually simulates trajectories which provide an atomic level view of the binding process. This is essential in our research because we need to simulate a molecule that will perfectly fit into the binding site.
After reading multiple papers on molecular dynamics and HIV-AIDS we decided to use the program “Maestro Schrodinger” to dock the molecules. We ran into a few issues with the server at Pace and it took us a few day to solve the issue. Currently, we are using “Amber Tutorials” to learn the Unix Command-Line. Even though it’s only been a few weeks I have been able to apply a lot of my Biology 101 and 102 knowledge and I have learned a lot about the HIV virus and molecular dynamics. I look forward to continuing this research project.