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Protein Sci. 2020 Jan;29(1):237-246. doi: 10.1002/pro.3773. Epub 2019 Nov 25.

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS.

Author information

1
Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.
2
Laboratoire de Biochimie Théorique, CNRS, Université de Paris, Paris, France.
3
Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
4
Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington.
5
Division of Applied Mathematics, Brown University, Providence, Rhode Island.

Abstract

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the Adaptive Poisson-Boltzmann Solver (APBS) software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two-dimensional external molecular visualization software. This process has inherent limitations: visualization of three-dimensional objects using a two-dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol-APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple graphical user interface (GUI) for either a standard desktop or immersive virtual reality experience.

KEYWORDS:

electrostatics; molecular visualization; solvation; virtual reality

PMID:
31710727
PMCID:
PMC6933841
[Available on 2021-01-01]
DOI:
10.1002/pro.3773

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