three javelinas and the big bad wolf!

DREU Summer 2011

My Summer in Albuquerque

Week 3: June 13 - June 17

This week I began looking at a new protein, 1QLP. It is much larger than both MHC and TCR. While MHC has 275 residuals and TCR has 200 residuals, 1QLP has 372 residuals. Because it is so large, it takes a long time to run, an average of 28 hours, compared to MHC's 3 hours and TCR's 1 hour. I once again began making roadmaps of 1QLP by adjusting the percentage of the protein that was flexible. However, the number of rejections for 1QLP was quite a bit higher than the rejections that were found when MHC and TCR were run. This was expected because 1QLP is so large, and it would have been surprising if the number of rejections for 1QLP were similar to the rejections for MHC and TCR. I also began working on code to create a roadmap for more than one articulated linkage. Articulated linkages are a better model for proteins, because proteins have joints that move in different ways. I started by comparing the differences between the code used to create a roadmap for one robot and to create a roadmap for multiple roadmaps, and then began to apply the same changes to the code used to create a roadmap for one articulated linkagae. Each robot has joints, so for the moment I am assuming all of the robots have the same number of joints, although in the future I will have to alter the code so that the robots can have different numbers of joints. Thursday we had a meeting about the application and advising process for graduate school. We talked to advisors and professors in the computer science department. Once again, it made me both nervous and excited about the prospect of graduate school in my future!

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