During this week at UCSD we continued our research and tested all of our hypothesis from the previous week! The first hypothesis that I tested was if the standard deviation of the distance between the center of mass of the ligand and the center of mass of the binding pocket. After lots of coding I was able to finally find the values and plot them over IC50 just to find that it had absolutely no correlation. After that I tested whether or not the RMSF of the binding pocket correlates to IC50 but again I found no correlation.
I decided to move away from testing the movements of the binding pocket and ligand and instead look at the bonds between the two. As I was looking though the VMD simulations I noticed that the total number of interactions between the ligand and protein may correspond to the effectiveness of the drug. Next week I will write a code to calculate the number of interactions and hopefully find a good correlation.
Outside of the lab I spent most of my time with Ry Gould and Wynton Brown for their last week in California and their last week of their internships. One of their last nights we went out to dinner at the beach club and afterwards saw some very tall palm trees.
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