Eargle John, Luthey-Schulten Zaida
Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
Comput Biol Chem. 2006 Jun;30(3):219-26. doi: 10.1016/j.compbiolchem.2006.01.004. Epub 2006 May 3.
An important part of protein structure characterization is the determination of excluded space such as fissures in contact interfaces, pores, inaccessible cavities, and catalytic pockets. We introduce a general tessellation method for visualizing the dual space around, within, and between biological molecules. Using Delaunay triangulation, a three-dimensional graph is constructed to provide a displayable discretization of the continuous volume. This graph structure is also used to compare the dual space of a system in two different states. Tessellator, a cross-platform implementation of the algorithm, is used to analyze the cavities within myoglobin, the protein-RNA docking interface between aspartyl-tRNA synthetase and tRNA(Asp), and the ammonia channel in the hisH-hisF complex of imidazole glycerol phosphate synthase.
蛋白质结构表征的一个重要部分是确定排除空间，如接触界面中的裂缝、孔隙、不可接近的腔和催化口袋。我们引入了一种通用的镶嵌方法，用于可视化生物分子周围、内部和之间的对偶空间。使用德劳内三角剖分法构建三维图，以提供连续体积的可显示离散化。这种图结构还用于比较系统在两种不同状态下的对偶空间。该算法的跨平台实现Tessellator，用于分析肌红蛋白中的腔、天冬氨酰-tRNA合成酶与tRNA（Asp）之间的蛋白质-RNA对接界面，以及咪唑甘油磷酸合酶的hisH-hisF复合物中的氨通道。
