Approximation algorithms for protein folding in the hydrophobic-polar model on 3D hexagonal prism lattice
Approximation algorithms for protein folding in the hydrophobic-polar model on 3D hexagonal prism lattice
复制标题
3D 六角棱柱晶格疏水极性模型中蛋白质折叠的近似算法
DOI：
10.1089/cmb.2017.0185
复制
发表时间：
2018
影响因子：
1.7
通讯作者：
Zhao Xu
中科院分区：
文献类型：
--
作者：
Qianghui Guo;Jian Wang;Zhao Xu
在这篇文章中，我们研究了三维（3D）六棱柱晶格上的疏水极性（HP）模型中的蛋白质折叠问题的近似算法。我们提出了两个近似算法的基础上以前的工作，二维（2D）正方形，三维立方，和二维六角晶格HP模型。第一种算法产生H-H接触主要在六边形平面上或六边形平面之间的褶皱，并且具有近似比[公式：见正文]。而在第二种算法生成的褶皱中，H-H接触主要发生在锯齿形平面上或锯齿形平面之间。第二种算法的理论近似比界不小于[公式：见正文]，虽然不比第一种算法好，但在实际应用中，对于特定情况，它可能会表现得更好。
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 [Formula: see text]. 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 [Formula: see text], although no better than the first algorithm, it may perform much better for specific instances in practice.