CalVSP: a program for analyzing the molecular surface areas, volumes, and polar surface areas

Abstract

The molecular volume, surface area, and polar molecular surface area are important descriptors for characterizing and predicting the molecular properties of lead compounds. Existing computational tools for calculating the above parameters often have complex workflows and are not well-suited for high-throughput conditions. CalVSP is an open-source software for computing molecular volume, molecular surface area, and polar surface area. The software implements a grid-based algorithm that dynamically optimizes grid spacing via quantum chemical reference data to ensure precise parameter calculations. CalVSP was tested on 9489 3D molecular structures, and the results revealed a mean absolute percentage error of 1.25% (95% CI: 1.23–1.27%) for the molecular volume and 1.33% (95% CI: 1.31–1.35%) for the molecular surface area compared with the quantum chemical data. For the molecular polar surface area calculations, the mean absolute percentage error was 4.59% (95% CI: 4.16–5.04%) across the 388 tested molecular structures. The CalVSP written in the C programming language offers a lightweight and easy tool. It can be integrated with other molecular property prediction tools to increase computational accuracy and for large-scale molecular calculations.