Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations
Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations
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DOI：
10.1016/0263-7855(95)00071-2
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发表时间：
1995-12-01
期刊：
影响因子：
--
通讯作者：
Doi, J
中科院分区：
文献类型：
--
作者：
Masuya, M;Doi, J
我们开发了一种基于数学形态学运算的数字方法，获得范德华表面、溶剂可及表面和分子表面三种类型的表面，提取分子表面和内部的空腔，并提取与空腔接触的配体部分。使用实体建模对分子表面、空腔和部分以及血红素区域进行可视化。该方法使我们能够获得空腔和抑制剂部分的体积以及表面面积。实体建模使我们能够获得任意位置的横截面。这在对接研究中具有相当大的实用性。
We developed a digital method based on mathematical morphological operations to obtain three types of surfaces: van der Waals surface, solvent-accessible surface, and molecular surface, to extract the cavities on the surface and interior part of the molecule and to extract the ligand portions in contact with the cavities. The molecular surface, the cavities and the portions, and the heme region are visualized using solid modeling.The method enables us to obtain the volumes of the cavities and inhibitor portions and the areas of the surfaces. Solid modeling enables us to obtain cross-sections at arbitrary positions. This will have considerable utility in docking studies.