Blog 2

These past few weeks, I have been working on familiarizing myself with molecular dynamics and understanding how big of a role they play with our research. Molecular dynamics is a computer based stimulation which helps analyze atoms and molecules that are moving and in which ways they interact with one another. This technique helps us work with protein models and experiment different methods of combining them. Protein modeling is a very effective way that helps obtain structural information before researchers start experimenting in labs. With the help of “Amber Tutorials” we can see the motion of protein models and be able to design different sets of proteins that are arranged in various ways with computer coding. MD stimulations aids in finding a more accurate model of the target protein and predict any changes in the function of the protein.

Dr.Deng has been very busy this semester so I have been working on reading up on how to use Amber and master all of its tutorials. I have ran into problems several times where the program either stops working or does not allow me to insert a certain set of codes therefore I ask Professor Deng for assistance and he is usually able to help me. Amber is not a very effective program but it is great for beginners to use and familiarize themselves with the coding language. Later on, we will start using better programs that aid us in protein stimulations.






Blog 1: Combining Docking and Molecular Dynamics- based free energy methods to improve computational screening of drug candidates against HIV integrase

Dr. Deng and I have been performing research to find better methods to improve screening of drug candidates against the HIV virus. We are using molecular dynamics and programs such as “Amber Tutorials” to help further guide us. Molecular dynamics is a computer based method to help us figure out how proteins fold and can bind to their targeted sites which is a crucial part of helping researchers figure out binding values for condensed directed locations. HIV is a human immunodeficiency virus that can destroy white blood cells and put one at risk for serious diseases/cancers. HIV integrase is a vital protein that will help us understand HIV’s role in the human body and how to target it specifically. We have been working on finding potential binding molecules of HIV integrase that will help predict ligand bound conformations and target proteins.

The past few weeks, we have been reading numerous articles/research papers and studying molecular dynamics to better understand how such viruses can be targeted. By practicing molecular dynamics simulations and analyzing data, we are getting one step closer to determining which drugs can bind easily. This research requires a lot of time and dedication because before using programs such as “Amber Tutorials”, one has to fully learn how it works and become comfortable with simple calculations and coding exercises. I have been able to apply previous knowledge to conduct docking simulations and analyze the protein models over the semester. I am excited to learn more throughout this school year and make it easier for other researchers to find drugs that can further prevent HIV related diseases.