title: Distances and classification of amino acids for different protein secondary structures.
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.
authors.affiliation: Institute of Theoretical Physics, Beijing 100080, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.forename: Li-mei
authors.initials: LM
authors.lastname: Zhang
authors.forename: Shan
authors.initials: S
authors.lastname: Guan
authors.forename: Wei-Mou
authors.initials: WM
authors.lastname: Zheng
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids; D019992:Databases as Topic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid
chemical_list: D000596:Amino Acids