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Computational biology, Microclusters, Proteins-Structure, Computer simulation, Three-dimensional imaging, Cluster, Rigidity, Flexibility, Modeling, Visualization
The exibility and rigidity of a protein structure is important for its function. Computational methods, such as those provided by KINARI-Web, Dr. Ileana Streinu's freely available server for protein rigidity analysis, can predict which regions of a protein are rigid and which are exible. It is of interest to both compare the rigidities of multiple variations of a protein structure and the results of using di erent computational and experimental methods for gaining information about this rigidity. While the former has important biological applications, the latter is essential for validation and better understanding of rigidity analysis. Previously, visual examination and analysis of these comparisons was di cult with KINARI-Web. In my thesis, I built on KINARI-Web to develop methods for comparative visualization of rigidity results. Based on these methods, I designed and implemented prototypes of three visualization tools: the Dilution, Mutation, and NMR Viewers, which involve biologically relevant applications of rigidity analysis to compare multiple variations of a structure. By using them to analyze the rigidity of several biological expamples, I demonstrated that these tools provide novel insights into this computational data.
Flynn, Emily R., "Comparing and visualizing in silico protein rigidity : methods and applications" (2014). Honors Project, Smith College, Northampton, MA.
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