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Distances and classification of amino acids for different protein secondary structures

Xin Liu·Li-mei Zhang·Shan Guan·Wei-Mou Zheng
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Abstract

Window profiles of amino acids in protein sequences are taken as a description of the amino acid environment. The relative entropy or Kullback-Leibler distance derived from profiles is used as a measure of dissimilarity for comparison of amino acids and secondary structure conformations. Distance matrices of amino acid pairs at different conformations are obtained, which display a non-negligible dependence of amino acid similarity on conformations. Based on the conformation specific distances clustering analysis for amino acids is conducted.

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Xin Liu, Li-mei Zhang, Shan Guan, Wei-Mou Zheng. 2003-06-16. Distances and classification of amino acids for different protein secondary structures. https://doi.org/10.1103/physreve.67.051927

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