MoloVol: an easy-to-use program to calculate various volumes and surface areas of chemical structures and identify cavities

20 September 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


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. MoloVol, 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. MoloVol 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 at reasonable timescales. MoloVol 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.


surface area

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