INRIA Sophia-Antipolis-Méditerranée, Algorithms-Biology-Structure, Sophia-Antipolis, France.
Bioinformatics. 2010 Apr 1;26(7):964-5. doi: 10.1093/bioinformatics/btq052. Epub 2010 Feb 7.
Intervor is a software computing a parameter-free representation of macro-molecular interfaces, based on the alpha-complex of the atoms. Given two interacting partners, possibly with water molecules squeezed in-between them, Intervor computes an interface model which has the following characteristics: (i) it identifies the atoms of the partners which are in direct contact and those whose interaction is water mediated, (ii) it defines a geometric complex separating the partners, the Voronoi interface, whose geometric and topological descriptions are straightforward (surface area, number of patches, curvature), (iii) it allows the definition of the depth of atoms at the interface, thus going beyond the traditional dissection of an interface into a core and a rim. These features can be used to investigate correlations between structural parameters and key properties such as the conservation of residues, their polarity, the water dynamics at the interface, mutagenesis data, etc.
Intervor can be run from the web site http://cgal.inria.fr/abs/Intervor or upon downloading the binary file. Plugins are also made available for VMD and Pymol.
Intervor 是一款软件，它基于原子的 alpha 复形，为大分子界面计算一个无参数的表示。对于两个相互作用的配体，可能有水分子被夹在它们之间，Intervor 计算出一个界面模型，该模型具有以下特点：（i）它识别直接相互作用的配体原子和那些通过水分子介导相互作用的原子，（ii）它定义了一个分离配体的几何复形，即 Voronoi 界面，其几何和拓扑描述是直接的（表面积、斑块数量、曲率），（iii）它允许定义界面处原子的深度，从而超越了传统的将界面剖分为核心区和边缘区的方法。这些特性可用于研究结构参数与关键性质之间的相关性，如残基的保守性、极性、界面处的水分子动力学、突变数据等。
Intervor 可以从网站 http://cgal.inria.fr/abs/Intervor 运行，也可以下载二进制文件后运行。还提供了 VMD 和 Pymol 的插件。
