This article is cited in 6 papers

Solvability problems in the protein secondary structure recognition

K. V. Rudakov^ab, I. Yu. Torshin<sup>c

a</sup> Moscow Institute of Physics and Technology
^b Dorodnitsyn Computing Centre of the Russian Academy of Sciences
^c Russian Center of the Trace Element Institute for UNESCO

Abstract: The purpose of the work is to develop a formalism for the application of the algebraic approach to recognition of the protein secondary structure. Paper presents rigorous formal description of the problem and considers its solvability, regularity, and locality. Key terms for the analysis of locality, such as a neighborhood, mask, mask system, monotony, and irreducibility of the mask systems were proposed. An algorithm for constructing nonredundant mask systems was formulated. The formalism has allowed to formulate a correct description of the hypothesis of the local character of the dependence of the secondary structure on the primary and to obtain constructive criteria of the solvability of the problem.

Keywords: algebraic approach; the secondary structure of protein; bioinformatics.