I had progress farther than what my mentor had expected. So today, when he had to go to a meeting for five hours, I was given two booklets so about MOE to help me fully understand the use of the program. I only had time to read about half of one of the booklet before my mentor got back, but it was enough time to learn more about MOE. I learned new features of MOE such as duplicating a ligand. That way I could experiment and change the chemical structure of the molecule and still have the original ligand to compare with. I was working with tarceva and rearranging its structure. I deleted and built new atoms to add to its components to see how the change would affect the newly made ligand. I new feature that I learn today on MOE is the pharmacophore query. However, I only know a little what a pharmacophore really is because I had a new assignment when I reached that part of the booklet.
My new assignment was to learn how to use CHARMM-GUI which is a program that is widely used for macromolecules like proteins. Although I began learning about this new program today, I believer that using it will be very difficult as it may be one of the most confusing program I have used yet.
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