用信息聚类方法研究蛋白质的氨基酸组成和二级结构含量的关系

The Relation between Amino Acid Composition and Secondary Structure Content of Protein Studied by Information Clustering Method

从蛋白质的氨基酸组成出发，用信息聚类方法给出了蛋白质的聚类树状图，发现树状图的分支与蛋白质二级结构的含量有较强的相关性．

The amino acid composition of each protein is viewed as a vector.Define the informaiton gain as the distance between each pair of vectors.By use of information clustering method a tree like diagram of the classification of 102 proteins is deduced in which 7 main branches (A to G) are obtained.A good relation between the clustering of amino acid composition and the classification of secondary structure contents are found.For example,the β type and α type of Nakashima′s classification of folding types correspond to branches D,G and E,B respectively,branch A corresponds to a part of α+β and α/β type,branches C and F-each contains two sub branches corresponding to type α+β and α/β and type α respectively,The ζ type corresponds to the scattered small branches in our clustering.In calculation,to improve statistics,we classify 20 amino acids into 15 categories (namely,I,L,V;F,W;S,T;and K,R merged into one respectively) according to the correlation between amino acid and secondary structure.On the otherhand,if the hydrophobic hydrophilic correlation between adjacent residues is taken into account in the clustering,then the result will be further improved.