Approximation Algorithms for Protein Folding in the Hydrophobic-Polar Model on 3D Hexagonal Prism Lattice

Journal of computational biology: A journal of computational molecular cell biology

QianghuiGuo^1¹  JianWang^2²  ZhaoXu^3³ 

[1] Department of Applied Mathematics, School of Mathematical Sciences, Nankai University, Tianjin, P.R. China^1;Department of Mathematics, Taiyuan University of Technology, Taiyuan, P.R. China^2;The Laboratory Equipment Department, Nankai University, Tianjin, P.R. China^3

关键词: hexagonal prism lattice;    HP model;    protein folding;   

DOI  :  10.1089/cmb.2017.0185

学科分类：生物科学（综合）

来源: Mary Ann Liebert, Inc. Publishers

【 摘 要 】

In this article, we study approximation algorithms for the protein folding problem in the hydrophobic-polar (HP) model on three-dimensional (3D) hexagonal prism lattice. We present two approximation algorithms based on previous work on two-dimensional (2D) square, 3D cubic, and 2D hexagonal lattice HP models. The first algorithm produces folds in which the H–H contacts are mainly on or between the hexagonal planes, and has approximation ratio . While in the folds produced by the second algorithm, the H–H contacts are mainly on or between the zigzag square planes. The theoretical approximation ratio bound of the second algorithm is no less than , although no better than the first algorithm, it may perform much better for specific instances in practice.

【 授权许可】

Unknown