Proteins as networks: usefulness of graph theory in protein science.
Proteins as networks: usefulness of graph theory in protein science.
复制标题
作为网络的蛋白质：图论在蛋白质科学中的用途。
DOI：
10.2174/138920308783565705
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发表时间：
2008
影响因子：
2.8
通讯作者：
A. Giuliani
中科院分区：
文献类型：
--
作者：
A. Krishnan;J. Zbilut;M. Tomita;A. Giuliani
网络范式基于通过将所研究系统表示为有向图来推导其新兴属性：任何系统都可以追溯到一组节点（其组成元素），这些节点通过与节点之间存在的关系相对应的边（弧）链接。这允许通过计算这些图的数学描述符（图论）来直接定量形式化系统。网络范式是特别有用的，当它是明确的建模系统的元素必须分别发挥作用的节点和弧，当拓扑约束有一个主要的作用，相对于动力。在这篇综述中，我们展示了如何节点和弧蛋白质拓扑结构的特点是在不同层次的定义：1。沿着序列的疏水性模式的递归矩阵2. 3D结构的α碳的接触矩阵3.分子动力学中分子各部分运动的相关矩阵。这三个条件代表不同的，但可能相关的网状系统，可以通过网络分析工具进行有益的分析。
The network paradigm is based on the derivation of emerging properties of studied systems by their representation as oriented graphs: any system is traced back to a set of nodes (its constituent elements) linked by edges (arcs) correspondent to the relations existing between the nodes. This allows for a straightforward quantitative formalization of systems by means of the computation of mathematical descriptors of such graphs (graph theory). The network paradigm is particularly useful when it is clear which elements of the modelled system must play the role of nodes and arcs respectively, and when topological constraints have a major role with respect to kinetic ones. In this review we demonstrate how nodes and arcs of protein topology are characterized at different levels of definition: 1. Recurrence matrix of hydrophobicity patterns along the sequence 2. Contact matrix of alpha carbons of 3D structures 3. Correlation matrix of motions of different portion of the molecule in molecular dynamics. These three conditions represent different but potentially correlated reticular systems that can be profitably analysed by means of network analysis tools.