Virtual reality (VR) technologies, typically in the context of game-playing, have changed the ways we interact with the virtual world. While integrating VR into scientific research is still very novel, we have found that a number of tasks are easier for humans to accomplish in VR compared to using traditional 2D user interfaces, particularly those that involve complex spatial manipulation. For instance, if a researcher is interested in studying a <i>specific </i>molecular transformation (e.g., a drug binding event), state-of-the-art interactive tools fusing high-performance computing, virtual reality, and real-time molecular dynamics enable researchers to interactively manipulate molecules with atomic-level precision, effectively “sketching” dynamical pathways for a complex structural rearrangement. The procedure is as follows: (1) a scientist utilizes interactive molecular dynamics in virtual reality (iMD-VR), where they can manipulate the molecules in order to undertake the transformation of interest; (2) the pathway is recorded for input into a dimensionality reduction routine; and (3) free energies are calculated along the reduced dimensional pathway. We have applied this idea to generate dynamical pathways for a range of different structural transformations where we ultimately wish to calculate free energies (biomolecular conformational changes, drugs binding to enzyme targets, and bond-breaking/making events). My work specifically focuses on dimensionality reduction methods which we have developed to analyze iMD-VR dynamical pathway “sketches” in order to generate information that map into more conventional molecular descriptors like bonds distances, torsions, angles, etc. I will illustrate the methodological approach through a number of application examples, including threading a methane molecule through a carbon nanotube, tying a 17-alanine chain in a knot, and several drugs binding to enzyme targets.  These methods have the potential to enable a new approach for molecular visualization, engineering and design.

Drug design using virtual reality: Free energy calculation of pathways generated from interactive molecular dynamics

2019 Fall National Meeting

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