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Protein tertiary structures exhibit an observable degeneracy in nature. This paper examines the connection between a protein motif's abundance in nature and its designability as measured by in silico methods. After generating a set of protein structures, we evaluated each structure's abundance in nature, ratio of possible contacts (contact degree) and in silico designability. Our results showed that any two or these metrics are moderately correlated. Together abundance and contact degree produced the strongest correlation with in silico designability. Our results suggest that abundance is indeed an indicator of designability. Furthermore, abundance and contact degree appear to correlate with some distinct components of in silico designability.
Senior Honors Thesis. Advisor: Gevorg Grigoryan.
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Rebecca G. Leong, "Why Do Protein Structures Recur?." Dartmouth Computer Science Technical Report TR2015-775, May 2015.
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