Becca Walters undocks & redocks the flu drug oseltamivir (tamiflu) into the binding pocket of the neuramanidase protein
We’ve just published a paper describing the use of interactive molecular dynamics in virtual reality (iMD-VR) for carrying out flexible protein-ligand docking, demonstrated through experiments carried out docking drug molecules into the binding pockets of trypsin, neuraminidase, and HIV-1 protease.
Our paper “Isness: Using Multi-Person VR to Design Peak Mystical-Type Experiences Comparable to Psychedelics” (doi:10.1145/3313831.3376649 & arxiv.2002.00940) has been recognized with a best paper award at the 2020 ACM CHI Conference on Human Factors in Computing! Less than 1% of all paper submissions receive this award, so it’s really exciting!
The paper describes our efforts adapting “Narupa” (our open source VR software platform) to elicit ‘mystical-type experiences’ comparable to those reported by participants in psychedelic psychotherapy sessions. It builds on a body of work by a number of researchers, including Prof. Roland Griffiths, a psychiatrist and neuroscientist at the Johns Hopkins Centre for Psychedelic & Consciousness Research, who has investigated both naturally occurring & drug-induced ‘mystical type experiences’, and also Dr. Robin Carhart-Harris at the Imperial College Centre for Psychedelic Research, who speculated in a March 2018 paper that psychedelics combined with VR might have therapeutic benefits in a neuro-psychopharmacology context.
We’re hard at work finalizing Narupa2, a massive rewrite of the Narupa VR framework which is pythonic on the back-end, and therefore should be much more customizable by our scientific colleagues. meanwhile enjoy this little a taster of some of the lovely new VR-enabled renderers that you can look forward to!
I’m super excited to announce that the European Research Commision (ERC) has agreed to fund a project which I pitched to them called NANOVR (NANOscale design using Virtual Reality) under their ‘Consolidator Grant’ scheme. The ERC’s generous financial support will commence in summer 2020, enabling us to continue our efforts developing the Narupa VR tools as open source community resources, and carry on exploring all sorts of interesting research applications across domains like biochemistry, materials engineering, and nanoscience!
The rise of machine learning (ML) has created an explosion in the potential strategies which may be used to learn from data in order to make scientific predictions. For physical scientists who wish to apply ML strategies to a particular domain, this has created a bewildering scenario, where it is difficult to make an a priori assessment of what strategy to adopt within a vast space of possibilities.
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Really excited to see work by Dr. Simon Bennie featured on the cover of this month’s issue of the Journal of Chemical Education. The paper, which you can access here, outlines how Narupa, our open-source VR-enabled interactive simulation framework, was applied to develop a computational laboratory exercise enabling undergraduate students to better understand the dynamics and interactions that guide drug-protein binding.
In The Doors of Perception, Aldous Huxley recounted his experience taking mescaline under the guidance of the psychiatrist Humphrey Osmond. He wrote how it enabled him to glimpse the intrinsic energetic luminosity of matter: “the miracle, moment by moment, of naked existence… flowers shining with their own inner light and all but quivering under the pressure of the significance with which they were charged… [even] the folds of my grey flannel trousers were charged with Isness.”
“Isness” is our latest VR research project, designed to explore how the Narupa VR tools can be adapted to enable participants to experience the energetic essence of matter, and elicit perceptual responses comparable to psychedelic experiences. You can read more in an open-access paper we’ve just posted to the arXiv!
Very excited to announce a beta release of the open-source Narupa VR-enabled builder, which allows the building, designing, and editing of molecules.
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Excited to report on work we’ve just posted to the arXiv, describing interactive molecular dynamics in virtual reality (iMD-VR) using the open-source Narupa framework as an efficient strategy for generating reversible protein-ligand binding and unbinding pathways.
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(c) Rachel Freire, Becca Rose, & the Intangible Realities Lab, licensed under CC-BY-SA 4.0
Following on from some preliminary work we published in early 2019, I had an amazing last few days in the Intangible Realities Laboratory, spending time with the fabulous E-textile artists Rachel Freire and Becca Rose making v3 of our open-source VR data gloves, which we have specifically designed to facilitate multi-person interaction of the sort required to carry out careful molecular manipulations during interactive simulations.
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