Stephen Lau - June 18, 2015

     Rather researching more about alanine scanning, I decided to look more into the protein receptor I would be using for the process.  I learned that 2MD (also known as VDZ) is a ligand for the VDR (Vitamin D receptor) but not it's natural one unlike the Vitamin D.  Similar to Vitamin D, 2MD has 3 potential hydrogen bonds rather 1 which can make a possible difference when binding to the VDR.  After learning more about the protein I would be using, I decided to try using the alanine scanning feature on MOE.  However, I'm not sure if I can  deducted the data it has processed as I'm still undergoing the technicalities and basic steps of MOE.  I do know that with the data gathered, I'm able to determine which residue (amino acid) proves  to be important for the receptor after substituting it with alanine.  Tomorrow I will color code the replaced amino acids whether they were important to the receptor and 2MD ligand or if alanine allows it to bind more easily and more efficiently.  I may even have time to do my readings the tomorrow...