Tangible physical models have an important place in the history of chemistry and biochemistry. Three-dimensional (3D) molecular models have been used as conceptual and educational tools dating back to at least von Hofmann in the 1860s. Now we are able to further our understanding by interacting with molecules in real time as they move using virtual reality (VR) technology. The multi-user VR framework has been developed by a joint team of computer science and chemistry researchers at the University of Bristol, in collaboration with developers at Interactive Scientific and Oracle Corporation, have used Oracle’s public cloud infrastructure to combine real-time molecular simulations with the latest VR technology.
The movie below shows a researcher taking hold of a fully solvated benzylpenicillin ligand and interactively guiding it to dock it within the active site of the TEM-1 β-lactamase enzyme (with both molecules fully flexible and dynamic) and generate the correct binding mode. The simulations make use of a plug-in that communicates with the GPU-accelerated molecular simulation package OpenMM via PLUMED, allowing models of the type used for conventional MD simulations to be used directly within the VR framework. Generating a benzylpenicillin docking pathway would be very difficult just using standard computer algorithms, but as can be seen in the movie, the VR framework is intuitive and easy to control, enabling the researcher to generate a physically meaningful path. Anybody wishing to try out the tasks described in the paper can download the software at https://isci.itch.io/nsb-imd, and launch their own cloud-hosted session.
‘Sampling molecular conformations and dynamics in a multi-user virtual reality framework‘ by Michael O’Connor, Helen M. Deeks, Edward Dawn, Oussama Metatla, Anne Roudaut, Matthew Sutton, Becca Rose Glowacki, Rebecca Sage, Philip Tew, Mark Wonnacott, Phil Bates, Adrian J. Mulholland and David R. Glowacki in Science Advances.