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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/., Author summary Proteins are microscopic machines that help maintain, defend, and regulate cells. Properly 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. Virtual reality (VR) is a powerful tool for studying protein structures. But many current systems for viewing molecules in VR, though effective, have challenging usability limitations. We have created a new web application called ProteinVR that overcomes these challenges. ProteinVR enables VR molecular visualization in users’ browsers, without requiring them to install a separate program or plugin. It runs on a broad range of desktop, laptop, and mobile devices. For users without VR headsets, ProteinVR leverages mobile-device orientation sensors or video-game-style keyboard navigation to provide an immersive experience. We release ProteinVR as open-source software and have posted a working version at http://durrantlab.com/pvr/.