Blog #2

Dr. Deng and I have been working on Amber Tutorials and test running the program “Maestro Schrodinger.” In order for me to utilize the program Maestro, I need to be proficient in all of the tutorials on Amber. Amber is a tool that teaches people how to use a molecular dynamics software. The first step was to learn the Unix Command-Line. From this tutorial I learned how to use the command line to navigate a file system, view directories view directories and copy, move, and remove files and directories. Then I did another tutorial which gave an introduction to Molecular Dynamics Simulations. This tutorial was extremely helpful because it gave me a better insight into what we are actually researching. This research is extremely beneficial to me because I get to see how the latest technology can be used in science today.


The last two weeks we actually ran into a lot of problems. Once we received the license from Maestro to use the system we were not able to register the program. Therefore, we contacted the company and are waiting for a response. We also had issues trying to connect to the server. We worked with the IT department to resolve most of the issue. Currently, I am working on 2 more tutorials. Even though Amber is a great program the site does not work that often. These obstacles have taught me that in research most of the time things do not go smoothly. We need to work together to resolve unforeseen issues and not give up. Dr. Deng and I are excited to finally be able to use Maestro. We will be continuing our research this upcoming fall semester.

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.