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.



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