Enumeration of Extended m-Regular Linear Stacks

• Published in: Journal of computational biology Vol. 23; no. 12; p. 943
• Main Authors: Guo, Qiang-Hui, Sun, Lisa H, Wang, Jian
• Format: Journal Article
• Language: English
• Published: United States 01.12.2016
• Subjects: Algorithms; Humans; Linear Models; Mathematical Concepts; Models, Molecular; Protein Folding; Proteins - chemistry; m$$-regular linear stack; protein fold; zigzag stack; contact map
• ISSN: 1557-8666
• DOI: 10.1089/cmb.2016.0041

The contact map of a protein fold in the two-dimensional (2D) square lattice has arc length at least 3, and each internal vertex has degree at most 2, whereas the two terminal vertices have degree at most 3. Recently, Chen, Guo, Sun, and Wang studied the enumeration of [Formula: see text]-regular linear stacks, where each arc has length at least [Formula: see text] and the degree of each vertex is bounded by 2. Since the two terminal points in a protein fold in the 2D square lattice may form contacts with at most three adjacent lattice points, we are led to the study of extended [Formula: see text]-regular linear stacks, in which the degree of each terminal point is bounded by 3. This model is closed to real protein contact maps. Denote the generating functions of the [Formula: see text]-regular linear stacks and the extended [Formula: see text]-regular linear stacks by [Formula: see text] and [Formula: see text], respectively. We show that [Formula: see text] can be written as a rational function of [Formula: see text]. For a certain [Formula: see text], by eliminating [Formula: see text], we obtain an equation satisfied by [Formula: see text] and derive the asymptotic formula of the numbers of [Formula: see text]-regular linear stacks of length [Formula: see text].