Backbone Conformational Pattern Clustering of Three-Dimensional Peptide Fragments of Proteins

抄録

In this paper we aim to examine in detail the data distribution within each conformational pattem class and to identify some local common structural features among the fragments in a particular cluster (or subcluster). Backbone conformational pattern clustering was carried out for the three-dimensional peptide fragments where the Φ-ψ, conformational pattern of the TA (target amino acid) belongs to class A (α-helix dominant class) or β(n-sheet dominant class) as defined in our previous work. The analysis for the fragments of class A suggested that these fragments involve four representative local backbone conformational patterns, not only for typical α-helix fragments but also for fragments closely related to type I turn or the starting moieties of α-helices. On the other hand, the analysis for class B fragments showed that these have much more diversity than class A fragments with respect to their local backbone structures. The details of the methods and results of the analyses are discussed here.