title: Condensed representations of protein secondary structure sequences and their application.
abstract: In this paper, we propose a nongraphical representation for protein secondary structures. By counting the frequency of occurrence of all possible four-tuples (i.e., four-letter words) of a protein secondary structure sequence, we construct a set of 3x3 matrices for the corresponding protein secondary structure sequence. Furthermore, the leading eigenvalues of these matrices are computed and considered as invariants for the protein secondary structure sequences. To illustrate the utility of our approach, we apply it to a set of real data to distinguish protein structural classes. The result indicates that it can be used to complement the classification of protein secondary structures.
authors.affiliation: Department of Applied Mathematics, Dalian University of Technology, Dalian, Liaoning 116024, P. R. China. fengjie0536@163.com
authors.forename: Jie
authors.initials: J
authors.lastname: Feng
authors.forename: Tian-ming
authors.initials: TM
authors.lastname: Wang
mesh_terms: D019295:Computational Biology / Q000379:methods; D017433:Protein Structure, Secondary; D011506:Proteins / Q000145:classification; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins