Surgical manipulation of real-time molecular simulations accelerates research tasks

Scientists at the University of Bristol, located in the UK, have developed new virtual reality (VR) cloud-based tools to help academics and industry progress new drugs, materials and boost the teaching of chemistry.

A joint team of computer science and chemistry researchers, in collaboration with developers at Bristol based start-up Interactive Scientific and Oracle Corporation, have used Oracle's public cloud infrastructure to combine real-time molecular simulations with the latest virtual reality technology.

This collaboration has made it possible for researchers to reach out and 'touch' molecules as they move -- folding them, knotting them, plucking them and changing their shape to test how they interact. Using cloud supercomputing, several people can interact with the molecules in the same virtual space at the same time. {module In-article}

Industry is already showing interest in using VR in this breakthrough way to change how drugs are designed, and to transform the teaching of chemical structures and dynamics.

For the research, published in Science Advances, the team designed a series of molecular tasks for participants to test on traditional mouse and keyboard, touchscreens and virtual reality. This included threading a small molecule through a nanotube, changing the screw-sense of a small organic helix and tying a small string-like protein into a simple knot.

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. For complex 3D tasks it was found that VR offers a significant advantage, and participants were ten times more likely to succeed in difficult tasks such as knot tying.

University of Bristol Professor of Chemistry Adrian Mulholland said: "Chemists have always made models of molecules to understand their structure -- from how atoms are bonded together to Watson and Crick's famous double helix model of DNA. At one point in their education, most people have held a molecular model, probably made from plastic or metal. Models like these are particularly important for things we can't see, such as the nanoscale world of molecules. 

"Thanks to this research we can now apply virtual reality to study a variety of molecular problems which are inherently dynamic, including binding drugs to its target, protein folding and chemical reactions. As simulations become faster we can now do this in real time which will change how drugs are designed and how chemical structures are taught."

Corresponding author and Royal Society Research Fellow Dr David Glowacki, who works jointly between Computer Science and Chemistry added: "Using VR to understand molecular structure and dynamics allows to perform a kind of nanoscale molecular "surgery," enabling researchers to develop an intuition for the dynamical 'feel' of specific molecular systems. The medical field has known for years that VR-trained surgeons complete procedures faster than non-VR trained counterparts, with significantly lower error rates. That's part of the reason why I think it's interesting to adapt this technology to understand nano-scale systems. A big reason I find this work so fascinating is because it requires unifying the state-of-the-art in technology with aesthetics, design and psychology."

Computer Science PHD student Michael O'Connor, one of the paper's lead authors, said: "Tying a molecule in a knot is represents a difficult 3d task. The traditional method for manipulating a molecule is to write programs that try to nudge it in the direction you want. For something as complicated as this, it would be extremely difficult to write such a program.

"Knots are physiologically interesting because hundreds of proteins have been found to exist in knotted structures, and it has become a puzzle to try and figure out how they get into these knotted forms. Using VR, we can explore these knotted structures, tying and untying them easily!"

"This research, supported by Oracle's Startup for Higher Education programme, demonstrates the kind of innovation that is now possible with Cloud -- in this case to accelerate nanotech research and drug discovery" said Phil Bates, an architect at Oracle Cloud. "Cloud is enabling scientists globally to collaborate, in real time, on complex molecular modelling and simulation challenges. This research is a great example of how academics are using Cloud to run research workloads that previously could only be supported with specialised supercomputers."

This work opens up exciting avenues for accelerating progress in molecular engineering and drug design by being able to collaboratively visualise and interact with the nanoscale. More broadly, the team's findings highlight the potential for VR in seeing and manipulating complex 3D structures, with applications across research, industry, and education.