Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Laureanti, Joseph; Brandi, Juan; Offor, Elvis; Engel, David; Rallo, Robert; Ginovska, Bojana; Martinez, Xavier; Baaden, Marc; Baker, Nathan A.

doi:10.1002/pro.3773

Title: Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS

Journal Article · Mon Nov 25 00:00:00 EST 2019 · Protein Science

DOI:https://doi.org/10.1002/pro.3773· OSTI ID:1575785

Laureanti, Joseph ^[1]; Brandi, Juan ^[1]; Offor, Elvis ^[1]; Engel, David ^[1]; Rallo, Robert ^[1]; Ginovska, Bojana ^[1]; Martinez, Xavier ^[2]; Baaden, Marc ^[2];

^[3]

Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory Richland Washington
Laboratoire de Biochimie Théorique CNRS, Université de Paris Paris France, Institut de Biologie Physico‐Chimique‐Fondation Edmond de Rothschild PSL Research University Paris France
Advanced Computing, Mathematics, and Data Division Pacific Northwest National Laboratory Richland Washington, 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.

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Sponsoring Organization:: USDOE

OSTI ID:: 1575785

Journal Information:: Protein Science, Journal Name: Protein Science Vol. 29 Journal Issue: 1; ISSN 0961-8368

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 16 works

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