LPTM, CNRS UMR 8089, Université Cergy-Pontoise, F-95302 Cergy-Pontoise, France.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W373-8. doi: 10.1093/nar/gkt509. Epub 2013 Jun 12.
Protein structures are an ensemble of atoms determined experimentally mostly by X-ray crystallography or Nuclear Magnetic Resonance. Studying 3D protein structures is a key point for better understanding protein function at a molecular level. We propose a set of accurate tools, for analysing protein structures, based on the reliable method of Voronoi-Laguerre tessellations. The Voronoi Laguerre Delaunay Protein web server (VLDPws) computes the Laguerre tessellation on a whole given system first embedded in solvent. Through this fine description, VLDPws gives the following data: (i) Amino acid volumes evaluated with high precision, as confirmed by good correlations with experimental data. (ii) A novel definition of inter-residue contacts within the given protein. (iii) A measure of the residue exposure to solvent that significantly improves the standard notion of accessibility in some cases. At present, no equivalent web server is available. VLDPws provides output in two complementary forms: direct visualization of the Laguerre tessellation, mostly its polygonal molecular surfaces; files of volumes; and areas, contacts and similar data for each residue and each atom. These files are available for download for further analysis. VLDPws can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/vldp.
蛋白质结构是通过 X 射线晶体学或核磁共振实验确定的原子集合。研究 3D 蛋白质结构是在分子水平上更好地理解蛋白质功能的关键点。我们提出了一组基于 Voronoi-Laguerre 镶嵌可靠方法的准确分析蛋白质结构的工具。Voronoi-Laguerre Delaunay 蛋白质网络服务器（VLDPws）首先对整个给定的系统进行 Laguerre 镶嵌计算，该系统首先嵌入溶剂中。通过这种精细的描述，VLDPws 提供了以下数据：（i）用高精度评估的氨基酸体积，这与实验数据的良好相关性得到了证实。（ii）在给定蛋白质内定义新的残基间接触。（iii）对溶剂中残基暴露的测量，在某些情况下显著改善了标准可及性概念。目前，没有等效的网络服务器可用。VLDPws 以两种互补的形式提供输出：Laguerre 镶嵌的直接可视化，主要是其多边形分子表面；体积文件；以及每个残基和每个原子的面积、接触和类似数据。这些文件可用于下载以进行进一步分析。VLDPws 可在 http://www.dsimb.inserm.fr/dsimb_tools/vldp 访问。
