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Measuring Uncertainty Of Protein Secondary Structure, Alan Eugene Herner

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This dissertation develops and demonstrates a method to measure the uncertainty of secondary structure of protein sequences using Shannon's information theory. This method is applied to a newly developed large dataset of chameleon sequences and to several protein hinges culled from the Hinge Atlas. The uncertainty of the central residue in each tripeptide is computed for each amino acid in a sequence using Cuff and Barton's CB513 as the reference set. It is shown that while secondary structure uncertainty is relatively high in chameleon regions [avg = 1.27 bits] it is relatively low in the regions 1-7 residues nearest a …