Maglic Jasmin B, Lavendomme Roy
Center for Geometrical Engineering of Cellular Systems, Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, 2100, Denmark.
Center for Ordered Materials, Organometallics and Catalysis (COMOC), Department of Chemistry, Ghent University, Krijgslaan 281-S3, Ghent, 9000, Belgium.
J Appl Crystallogr. 2022 Jun 23;55(Pt 4):1033-1044. doi: 10.1107/S1600576722004988. eCollection 2022 Aug 1.
Cavities are a ubiquitous feature of chemical structures encountered in various fields ranging from supramolecular chemistry to molecular biology. They are involved in the encapsulation, transport and transformation of guest molecules, thus necessitating a precise and accessible tool for estimating and visualizing their size and shape. , a free user-parametrizable open-source software, developed for calculating a range of geometric features for both unit-cell and isolated structures, is presented here. utilizes up to two spherical probes to define cavities, surfaces and volumes. The program was optimized by combining an octree data structure with voxel-partitioned space, allowing for even high-resolution protein structure calculations on reasonable timescales. comes with a user-friendly graphic interface along with a command-line interface for high-throughput calculations. It was written in C++ and is available on Windows, macOS and Linux distributions.
空洞是从超分子化学到分子生物学等各个领域中化学结构普遍存在的特征。它们参与客体分子的包封、运输和转化，因此需要一种精确且易于使用的工具来估计和可视化它们的大小和形状。这里介绍了一种免费的、用户可参数化的开源软件，它是为计算晶胞和孤立结构的一系列几何特征而开发的。该软件利用多达两个球形探针来定义空洞、表面和体积。通过将八叉树数据结构与体素划分空间相结合对该程序进行了优化，从而能够在合理的时间尺度上进行高分辨率蛋白质结构计算。该软件具有用户友好的图形界面以及用于高通量计算的命令行界面。它是用C++编写的，可在Windows、macOS和Linux发行版上使用。
