BACK TO PROJECT PAGE
July 8th
Today I found a few papers on using SOMS to predict the secondary structure of a protein shape based on the amino acid sequence. I found a lot of papers that deal with classifying proteins into certain families based on their amino acid sequence using self- organization.
July 9th
I used the SOM toolbox for MATLAB, which I downloaded from the following website: http://www.cis.hut.fi/projects/somtoolbox/download/ , to look at demos. I want to be able to use MATLAB to show the 3-dimensionality of a protein. Now itís not going to look like the actual protein, as long as the program can distinguish between two different shapes. I found three demos that all produce visual graphs based on input data. The input data is ASCII formatted.
July 10th
I started analyzing the ASCII files to see if I could convert my binary amino acid sequences so the computer will understand the data. I also started brainstorming on how else I could encode the sequence. I still canít decide if I want to use C++ or MATLAB. I definitely want to use MATLAB and the SOM toolbox to show the protein. I think I might use C++ to recognize the amino acid sequence patterns. I think for this project MATLAB will work better because it shows incredible detail with the graph and that is very important when looking at proteins.
July 11th
Today my mom came to pick me up and I went home for the weekend. I could have driven home by myself but I would have gotten lost. I always get lost but then I eventually find my way back. So we drove four and half hours and I went straight to my bed. This was the first time I was away from home for such a long time. I know a month is not a long time, but compared to a week it is. It was nice to come back home for a little while.
July 12th
Today I went to the beach with my friends. The beach where I live could be so beautiful if the sand wasnít actually red clay. It made me appreciate the beach near UMASSD. Thatís when it dawned on me; I left my laptop in my dorm room. I knew that when I was packing I would forget something. So every time I had an idea for the project I had to resort to paper, oh my how technology has spoiled society. I spent the rest of the day with my family.
July 13th
Today I went to a goodbye party for one of my friends. I had to leave early because tomorrow I am going back to UMASSD.
July 14th
My parents and I left the house at 7AM. It took only 3 and half hours to get here this time. It is very odd how it takes an extra hour and a half to get back to New York. Then my parents went home and I started to get all of these ideas for the project. I started thinking how I could use all three SOM programs to compare the proteins.
July 15th
Today I began organizing my references for the paper on protein shape prediction. This paper is different than the last two papers because this paper is based around ongoing projects being conducted by researchers all around the globe. The structure of a protein is very important to its function. Many proteins have certain shapes so they can bind to a unique substrate to perform a task. Biologists try to make designer drugs that can mimic the shape of a protein in order to duplicate the function of that protein. This is very important for people with protein deficiencies. However the problem with this is that after a protein binds it undergoes a conformational change. A major part of computer science/biology is to try to predict the new shape of the protein.
CONTINUE LOOKING AT LOG ENTRIES
BACK TO LOG ENTRIES
