Voro3D：应用于蛋白质结构的三维沃罗诺伊镶嵌
Voro3D: 3D Voronoi tessellations applied to protein structures.
作者信息
Dupuis Franck, Sadoc Jean-François, Jullien Rémi, Angelov Borislav, Mornon Jean-Paul
机构信息
Laboratoire de Minéralogie Cristallographie Paris, CNRS UMR 7590 Universités Paris 6 et 7, case 115, 4 Place Jussieu, 75252 Paris, France.
出版信息
Bioinformatics. 2005 Apr 15;21(8):1715-6. doi: 10.1093/bioinformatics/bth365. Epub 2004 Jun 24.
UNLABELLED
Voro3D is an original easy-to-use tool, which provides a brand new point of view on protein structures through the three-dimensional (3D) Voronoi tessellations. To construct the Voronoi cells associated with each amino acid by a number of different tessellation methods, Voro3D uses a protein structure file in the PDB format as an input. After calculation, different structural properties of interest like secondary structures assignment, environment accessibility and exact contact matrices can be derived without any geometrical cut-off. Voro3D provides also a visualization of these tessellations superimposed on the associated protein structure, from which it is possible to model a polygonal protein surface using a model solvent or to quantify, for instance, the contact areas between a protein and a ligand.
AVAILABILITY
The software executable file for PC using Windows 98, 2000, NT, XP can be freely downloaded at http://www.lmcp.jussieu.fr/~mornon/voronoi.html
CONTACT
franck.dupuis@sanofi-aventis.com; jean-paul-mornon@imcp.jussieu.fr.
未标注
Voro3D是一款原创的易于使用的工具，它通过三维（3D）沃罗诺伊镶嵌为蛋白质结构提供了全新的视角。为了通过多种不同的镶嵌方法构建与每个氨基酸相关的沃罗诺伊单元，Voro3D使用PDB格式的蛋白质结构文件作为输入。计算后，可以得出诸如二级结构分配、环境可及性和精确接触矩阵等不同的感兴趣的结构属性，而无需任何几何截断。Voro3D还提供了这些镶嵌与相关蛋白质结构叠加的可视化，从中可以使用模型溶剂对多边形蛋白质表面进行建模，或者例如量化蛋白质与配体之间的接触面积。
可用性
适用于使用Windows 98、2000、NT、XP的PC的软件可执行文件可从http://www.lmcp.jussieu.fr/~mornon/voronoi.html免费下载。
联系方式
franck.dupuis@sanofi-aventis.com；jean-paul-mornon@imcp.jussieu.fr。
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