Commercialisation of VR for biomolecular design
Lead Research Organisation:
University of Bristol
Department Name: Chemistry
Abstract
A market opportunity exists to build upon the outputs of successful BBSRC-funded research, which has developed tools for interactive molecular simulation, visualisation, manipulation and building in virtual reality (VR). This technology has the opportunity to transform commercially important areas such as structure-based drug design, molecular synthetic biology and protein engineering for practical applications. We are seeking 18 months of funding to support the initial stages of commercialisation activities to construct a spin-out company that sells a set of ready-to-market technologies that allow scientists within the biomolecular industry to transform their research pipelines.
Our software, Narupa, is a suite of VR-enabled software packages for molecular modelling and design. Narupa allows scientists to step into the molecular world to simulate, manipulate and build biomolecular systems. Our core software offering, Narupa iMD-VR, uniquely enables scientists to not only to view molecular systems but to also interact with running simulations and maniplate structures and interactions in real time. The simulations are dynamic, physically rigorous, flexible and fast, and can easily accommodate new molecular systems. It is multiuser, allowing teams to work together, proving new ways to collaborate (including virtually) on molecular design and engineering problems. We have demonstrated the effectiveness of the approach in user tests for molecular modelling tasks; it outperforms current tools.
These software tools have the potential to enable industrial biomolecular research to accelerate workflows and cut costs in ways that could not be envisaged even five years ago. We intend to utilise a unique combination of cloud computing, real-time research-grade simulation engines, and virtual reality (VR) to disrupt research across several areas, including synthetic chemistry, biochemistry, catalysis, drug design, and materials research. Narupa also provides a virtual meeting place for scientists to simultaneously inhabit the same simulation and share insights and collaborate in a way never possible before, and facilitate communication between experts and non-specialists.
The power of our tools and approach has been recognised by companies such as BP, Hyundai and Oracle, who have invested in research projects with us.
The opportunity to couple new immersive modes of computer-human interaction with scalable computing resources offers a short window for UK companies to emerge as global leaders in established fields that are otherwise difficult to disrupt. The bio-sector's R&D activities are significant components of UK economic output and are critical to ensuring the UK's standing in the global knowledge, research, and manufacturing economy. We estimate that there is a potential 8x ROI in R&D processes by the adoption of such tools, allowing scientists to rapidly test ideas and design hypotheses.
Funding from BBSRC will allow us to build on current successful industrial-academic contracts and to develop a commercial entity. The initial stages focus on outreach, comms and visiting industry partners for application scoping and demonstrating initial VR installations and business-specific uses. We will take a three-strand approach to achieve commercial success:
1) Offer fully supported VR installations for customers intending to build labs (we already have two commercial partners and over two dozen academic partner universities).
2) Dedicated consultancy for using VR for, accelerated dynamics simulations, visualisation and scientific applications.
3) Sales of cloud credits to link various existing software packages as well as a multi-user VR teleconference allowing remote scientific collaboration.
By the conclusion of the funding period, we will have constructed the framework for a sustainable business, secured venture capital funding in order to scale up this company and will have built a customer base.
Our software, Narupa, is a suite of VR-enabled software packages for molecular modelling and design. Narupa allows scientists to step into the molecular world to simulate, manipulate and build biomolecular systems. Our core software offering, Narupa iMD-VR, uniquely enables scientists to not only to view molecular systems but to also interact with running simulations and maniplate structures and interactions in real time. The simulations are dynamic, physically rigorous, flexible and fast, and can easily accommodate new molecular systems. It is multiuser, allowing teams to work together, proving new ways to collaborate (including virtually) on molecular design and engineering problems. We have demonstrated the effectiveness of the approach in user tests for molecular modelling tasks; it outperforms current tools.
These software tools have the potential to enable industrial biomolecular research to accelerate workflows and cut costs in ways that could not be envisaged even five years ago. We intend to utilise a unique combination of cloud computing, real-time research-grade simulation engines, and virtual reality (VR) to disrupt research across several areas, including synthetic chemistry, biochemistry, catalysis, drug design, and materials research. Narupa also provides a virtual meeting place for scientists to simultaneously inhabit the same simulation and share insights and collaborate in a way never possible before, and facilitate communication between experts and non-specialists.
The power of our tools and approach has been recognised by companies such as BP, Hyundai and Oracle, who have invested in research projects with us.
The opportunity to couple new immersive modes of computer-human interaction with scalable computing resources offers a short window for UK companies to emerge as global leaders in established fields that are otherwise difficult to disrupt. The bio-sector's R&D activities are significant components of UK economic output and are critical to ensuring the UK's standing in the global knowledge, research, and manufacturing economy. We estimate that there is a potential 8x ROI in R&D processes by the adoption of such tools, allowing scientists to rapidly test ideas and design hypotheses.
Funding from BBSRC will allow us to build on current successful industrial-academic contracts and to develop a commercial entity. The initial stages focus on outreach, comms and visiting industry partners for application scoping and demonstrating initial VR installations and business-specific uses. We will take a three-strand approach to achieve commercial success:
1) Offer fully supported VR installations for customers intending to build labs (we already have two commercial partners and over two dozen academic partner universities).
2) Dedicated consultancy for using VR for, accelerated dynamics simulations, visualisation and scientific applications.
3) Sales of cloud credits to link various existing software packages as well as a multi-user VR teleconference allowing remote scientific collaboration.
By the conclusion of the funding period, we will have constructed the framework for a sustainable business, secured venture capital funding in order to scale up this company and will have built a customer base.
Organisations
Publications
Amaro RE
(2020)
Biomolecular Simulations in the Time of COVID19, and After.
in Computing in science & engineering
Amaro RE
(2020)
A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19.
in Journal of chemical information and modeling
Amos STA
(2021)
Membrane Interactions of a-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR.
in The journal of physical chemistry. B
Ansell TB
(2021)
Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations.
in Journal of chemical theory and computation
Arcus VL
(2020)
Enzyme evolution and the temperature dependence of enzyme catalysis.
in Current opinion in structural biology
Arcus VL
(2020)
Temperature, Dynamics, and Enzyme-Catalyzed Reaction Rates.
in Annual review of biophysics
Ashraf S
(2021)
Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach.
in Scientific reports
| Description | | A virtual reality (VR) platform developed by researchers at the University of Bristol is allowing chemists, computational scientists and structural biologists to collaboratively design molecules like engineers create airplane components. "It's bringing human intuition to bear in a new way," according to Adrian Mulholland, a professor in the university's Centre for Computational Chemistry. The newest task for the interactive molecular dynamics simulations in VR (iMD-VR) tool is to help a seven-member team at the University of Bristol predict how potential drugs will bind to the coronavirus disease 2019 (COVID-19) targets, Mulholland says. "It's amazing how quickly the international scientific community has responded to the COVID-19 outbreak," he adds. "Structures of proteins from the virus have been solved by X-ray crystallography and Google DeepMind has predicted the structure of other [culprit] proteins, and people are starting to try to assemble models of the virus." VR has been touted as a drug development tool for two decades but dismissed by some scientists as little more than a toy for looking at molecules and proteins, "not a genuine research or education tool," Mulholland says. Sentiments have been changing with the maturation of VR and its application in training everyone from surgeons to architects. Gaming technology has been the big game changer when it comes to using VR for structure-based drug design, he continues, with the development of VR technology such as Facebook's Oculus. "We are now able to not just look at a molecule but also to manipulate it." Many small-molecule drugs work by binding to proteins, thereby stopping a virus from reproducing, but they need to be precisely positioned to fit snugly to their biological targets, he explains. The cost of setting up a VR system has also come down dramatically from a million-dollar investment in large, three-dimensional immersive spaces to about $5,000 for an iMD-VR setup to cover the cost of the hardware (one headset and a set of paddles) and graphics card to run simulations. The system is based on free, open-source software (Narupa interface), described last year in the Journal of Chemical Physics, and uses easily accessible room-scale VR headsets, such as the HTC Vive, says Mulholland. What makes the iMD-VR tool unique is that it enables multiple users to be in the same virtual environment, enabling collaboration across labs and geographies, he says. Its lead developer is David R. Glowacki, a research fellow at the University of Bristol with a joint position in chemistry and computer science. Hundreds of people have done user tests of the technology, many at industry conferences. Use of VR is taking off at universities around the world. Nanome has a VR docking program it describes as a "Minecraft for matter" that researchers are using to visualize and directly manipulate atoms, molecules and proteins. The lab of Jacob Durrant, an assistant professor of computer-aided drug design at the University of Pittsburgh, is developing VR software enabling students and researchers to walk around, and through, their favorite proteins, Mulholland says. The University of Tromsø in Norway has a dedicated VR lab and one is being built at the University of Copenhagen, he cites as examples. It won't be long before VR is the customary way drug designers work on many drug development problems, Mulholland predicts. Being able to view small molecules as three-dimensional objects simplifies the task of modifying them so they more tightly fit within the "keyhole" of a protein binding site. In a recent study published in PLOS One, University of Bristol researchers demonstrated that even in the hands of nonexperts the iMD-VR system could be used to easily dock a small drug molecule to influenza neuraminidase and HIV protease, recreating the binding poses hypothesized by X-ray crystallography. In previous work, Mulholland, Glowacki and coworkers carried out user tests that showed that iMD-VR was better for molecular modelling tasks than traditional computer-and-mouse methods. It's likely that the newer technology performs much better because it's the more intuitive way to deal with a molecule, he adds. "You really get a sense of [a molecule's] three-dimensional structure and literally reach out and grab each end and move it with your hands, and you can also walk around the problem." iMD-VR users in the study were able to accurately unbind and rebind drugs from protein targets in less than five minutes of real time, he notes. It's the combination of VR with interactive molecular dynamics that makes all the difference-a drug design process he likens to playing the Nintendo game 3D Tetris. "Using human intuition and a bit of chemistry knowledge [anyone] can do a real good job in VR of predicting how a drug binds." Educational Value Using iMD-VR requires "almost no training at all," says Mulholland. After a brief demonstration, undergraduate students in a teaching lab at the University of Bristol can effectively use a VR headset and paddles to manipulate molecules and learn how they bind to proteins. Even high school students have completed sophisticated molecular modeling tasks "relatively easily and well." Plastic models of molecules traditionally used in chemistry class are quite informative but can break and don't move properly, says Mulholland. With iMD-VR, students can "physically and correctly see how molecules behave, how they move and how they react" either by using the tool themselves or watching a live demonstration by their instructor. "In principle, everyone could be manipulating the same molecule at the same time." In Mulholland's lab, iMD-VR is currently being used for binding molecules to proteins involved in antibiotic resistance as well as to find drugs for COVID-19. In collaboration with BP, researchers are also modeling catalysts in VR trying to understand how to make molecules in cleaner processes, consuming less energy and generating less waste (aka "green chemistry"), he says. Two years ago, with support from Oracle, University of Bristol researchers were using VR cloud-based tools that allowed several people to interact with molecules in the same virtual space at the same time, says Mulholland. It successfully demonstrated that a simulation run in Frankfurt on Oracle Cloud Infrastructure at the company's German center could be visualized in Bristol, allowing geographically dispersed scientists to collaborate on molecular modeling tasks. The University of Bristol subsequently did some interactive data sharing with other universities, he adds, and is looking to build on this model. Such collaborations benefit from cloud mounting of the framework and sharing of computational resources. |
| Exploitation Route | | A virtual reality (VR) platform developed by researchers at the University of Bristol is allowing chemists, computational scientists and structural biologists to collaboratively design molecules like engineers create airplane components. "It's bringing human intuition to bear in a new way," according to Adrian Mulholland, a professor in the university's Centre for Computational Chemistry. The newest task for the interactive molecular dynamics simulations in VR (iMD-VR) tool is to help a seven-member team at the University of Bristol predict how potential drugs will bind to the coronavirus disease 2019 (COVID-19) targets, Mulholland says. "It's amazing how quickly the international scientific community has responded to the COVID-19 outbreak," he adds. "Structures of proteins from the virus have been solved by X-ray crystallography and Google DeepMind has predicted the structure of other [culprit] proteins, and people are starting to try to assemble models of the virus." VR has been touted as a drug development tool for two decades but dismissed by some scientists as little more than a toy for looking at molecules and proteins, "not a genuine research or education tool," Mulholland says. Sentiments have been changing with the maturation of VR and its application in training everyone from surgeons to architects. Gaming technology has been the big game changer when it comes to using VR for structure-based drug design, he continues, with the development of VR technology such as Facebook's Oculus. "We are now able to not just look at a molecule but also to manipulate it." Many small-molecule drugs work by binding to proteins, thereby stopping a virus from reproducing, but they need to be precisely positioned to fit snugly to their biological targets, he explains. The cost of setting up a VR system has also come down dramatically from a million-dollar investment in large, three-dimensional immersive spaces to about $5,000 for an iMD-VR setup to cover the cost of the hardware (one headset and a set of paddles) and graphics card to run simulations. The system is based on free, open-source software (Narupa interface), described last year in the Journal of Chemical Physics, and uses easily accessible room-scale VR headsets, such as the HTC Vive, says Mulholland. What makes the iMD-VR tool unique is that it enables multiple users to be in the same virtual environment, enabling collaboration across labs and geographies, he says. Its lead developer is David R. Glowacki, a research fellow at the University of Bristol with a joint position in chemistry and computer science. Hundreds of people have done user tests of the technology, many at industry conferences. Use of VR is taking off at universities around the world. Nanome has a VR docking program it describes as a "Minecraft for matter" that researchers are using to visualize and directly manipulate atoms, molecules and proteins. The lab of Jacob Durrant, an assistant professor of computer-aided drug design at the University of Pittsburgh, is developing VR software enabling students and researchers to walk around, and through, their favorite proteins, Mulholland says. The University of Tromsø in Norway has a dedicated VR lab and one is being built at the University of Copenhagen, he cites as examples. It won't be long before VR is the customary way drug designers work on many drug development problems, Mulholland predicts. Being able to view small molecules as three-dimensional objects simplifies the task of modifying them so they more tightly fit within the "keyhole" of a protein binding site. In a recent study published in PLOS One, University of Bristol researchers demonstrated that even in the hands of nonexperts the iMD-VR system could be used to easily dock a small drug molecule to influenza neuraminidase and HIV protease, recreating the binding poses hypothesized by X-ray crystallography. In previous work, Mulholland, Glowacki and coworkers carried out user tests that showed that iMD-VR was better for molecular modelling tasks than traditional computer-and-mouse methods. It's likely that the newer technology performs much better because it's the more intuitive way to deal with a molecule, he adds. "You really get a sense of [a molecule's] three-dimensional structure and literally reach out and grab each end and move it with your hands, and you can also walk around the problem." iMD-VR users in the study were able to accurately unbind and rebind drugs from protein targets in less than five minutes of real time, he notes. It's the combination of VR with interactive molecular dynamics that makes all the difference-a drug design process he likens to playing the Nintendo game 3D Tetris. "Using human intuition and a bit of chemistry knowledge [anyone] can do a real good job in VR of predicting how a drug binds." Educational Value Using iMD-VR requires "almost no training at all," says Mulholland. After a brief demonstration, undergraduate students in a teaching lab at the University of Bristol can effectively use a VR headset and paddles to manipulate molecules and learn how they bind to proteins. Even high school students have completed sophisticated molecular modeling tasks "relatively easily and well." Plastic models of molecules traditionally used in chemistry class are quite informative but can break and don't move properly, says Mulholland. With iMD-VR, students can "physically and correctly see how molecules behave, how they move and how they react" either by using the tool themselves or watching a live demonstration by their instructor. "In principle, everyone could be manipulating the same molecule at the same time." In Mulholland's lab, iMD-VR is currently being used for binding molecules to proteins involved in antibiotic resistance as well as to find drugs for COVID-19. In collaboration with BP, researchers are also modeling catalysts in VR trying to understand how to make molecules in cleaner processes, consuming less energy and generating less waste (aka "green chemistry"), he says. Two years ago, with support from Oracle, University of Bristol researchers were using VR cloud-based tools that allowed several people to interact with molecules in the same virtual space at the same time, says Mulholland. It successfully demonstrated that a simulation run in Frankfurt on Oracle Cloud Infrastructure at the company's German center could be visualized in Bristol, allowing geographically dispersed scientists to collaborate on molecular modeling tasks. The University of Bristol subsequently did some interactive data sharing with other universities, he adds, and is looking to build on this model. Such collaborations benefit from cloud mounting of the framework and sharing of computational resources. |
| Sectors | Chemicals,Creative Economy,Digital/Communication/Information Technologies (including Software),Education,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| URL | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228461 |
| Description | Research data and policy |
| Geographic Reach | National |
| Policy Influence Type | Contribution to new or improved professional practice |
| URL | https://www.chemistryworld.com/news/ukri-finds-itself-in-hot-water-too-over-researchfish-cyberbullyi... |
| Description | UKRI research data capture approaches |
| Geographic Reach | National |
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| URL | https://www.researchprofessionalnews.com/rr-news-uk-research-councils-2023-1-researchfish-tweets-aga... |
| Description | Oracle for Research Cloud Fellowship |
| Amount | $100,000 (USD) |
| Organisation | Oracle Corporation |
| Sector | Private |
| Country | United States |
| Start | 02/2023 |
| End | 12/2023 |
| Description | PREDACTED Predictive computational models for Enzyme Dynamics, Antimicrobial resistance, Catalysis and Thermoadaptation for Evolution and Desig |
| Amount | € 2,482,332 (EUR) |
| Funding ID | 101021207 |
| Organisation | European Research Council (ERC) |
| Sector | Public |
| Country | Belgium |
| Start | 10/2021 |
| End | 09/2026 |
| Description | https://gtr.ukri.org/person/2A2990B1-E1E1-4888-8848-7C256C3A3B43 |
| Amount | £20,009,000 (GBP) |
| Funding ID | https://gtr.ukri.org/person/2A2990B1-E1E1-4888-8848-7C256C3A3B43 |
| Organisation | United Kingdom Research and Innovation |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2006 |
| End | 02/2033 |