I spent most of this week doing background reading for the project. I also met Brian, the grad student I will be working for this summer. Thank goodness for him, he explains things very well and has definitely helped me to understand the reading I have been given. From what I have been told so far, I will be working with Brian on a computer program that compares protein structures. Ideally this type of program will one day be able to compare a protein of known structure and functionality to one of unknown functionality and determine the functionally significant amino acids in the latter protein's sequence.
The first half of my reading was on a study done by one of our collaborators, Dr. Olivier called Evolutionary Trace. Basically, Evolutionary Trace presumes that the most functionally significant amino acids will mutate the least. Consequently, by looking at a family of proteins, one can determine which amino acids are most significant by studying which amino acids are the most prevalent and unchanged throughout the proteins.
The second set of papers I read was on Geometric Hashing, a method developed by Y. Lamdan and H. Wolfson to recognize 3-D structures without having to compare each pixel of the structure to every pixel of the screen's view. This method is used to compare two proteins 3-D structures to recognize the functionally relevant sequences.