MoloVol : an easy-to-use program for analyzing cavities, volumes and surface areas of chemical structures.
Jasmin B MaglicRoy LavendommePublished in: Journal of applied crystallography (2022)
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 on 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.
Keyphrases
- high resolution
- high throughput
- density functional theory
- quality improvement
- molecular dynamics
- single cell
- molecular dynamics simulations
- monte carlo
- mass spectrometry
- living cells
- single molecule
- small molecule
- electronic health record
- stem cells
- big data
- fluorescence imaging
- protein protein
- deep learning
- water soluble
- biofilm formation
- amino acid
- escherichia coli
- photodynamic therapy
- drug discovery
- liquid chromatography