Abstract
Protein structure determines biological function. Accurately conceptualizing 3D protein/ligand structures is thus vital to scientific research and education. Virtual reality (VR) enables protein visualization in stereoscopic 3D, but many VR molecular-visualization programs are expensive and challenging to use; work only on specific VR headsets; rely on complicated model-preparation software; and/or require the user to install separate programs or plugins. Here we introduce ProteinVR, a web-based application that works on various VR setups and operating systems. ProteinVR displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space. Our web-based implementation is ideal for hypothesis generation and education in research and large-classroom settings. We release ProteinVR under the open-source BSD-3-Clause license. A copy of the program is available free of charge from http://durrantlab.com/protein-vr/, and a working version can be accessed at http://durrantlab.com/pvr/.
Highlights
Molecular visualization can provide structural, biological, and pharmacological insights that cannot be obtained in any other way
Understanding the three-dimensional structures of these machines–as well as the small molecules that interact with them–can advance scientific fields ranging from basic molecular biology to drug discovery
ProteinVR uses native web technologies, so it does not require users to download or install any programs or plugins beyond the web browser itself. In this sense it differs from other Virtual reality (VR) molecular-visualization programs [7, 8, 10, 11, 19,20,21,22], which require users to download a stand-alone program that may not be compatible with all operating systems
Summary
Molecular visualization can provide structural, biological, and pharmacological insights that cannot be obtained in any other way. Standard molecular-visualization computer programs, e.g., VMD [2] and PyMOL [3], improve 3D understanding by projecting 3D models onto 2D screens, allowing users to rotate and examine them in a faux 3D environment [2,3,4,5,6]. These visualizations are still only approximations of the true 3D structures—pictures of things, rather than the things themselves [7]. Perceiving the spatial arrangements of interacting moieties continues to be challenging in some contexts
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