Distances and classification of amino acids for different protein secondary structures.
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.
Liu
Xin
X
Institute of Theoretical Physics, Beijing 100080, China.
Zhang
Li-mei
LM
Guan
Shan
S
Zheng
Wei-Mou
WM
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
D000596:Amino Acids