Abstract
Window profiles of amino acids in protein sequences are used to describe the amino acid environment. The relative entropy or Kullback-Leibler distance derived from these 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, a clustering analysis for amino acids is conducted.
- Received 18 December 2002
DOI:https://doi.org/10.1103/PhysRevE.67.051927
©2003 American Physical Society