Software company Nanome has built a software platform that chemists and other researchers can use to build and experiment with molecules in virtual reality.
Image: Nanome

Chemists may be one of the first researchers to see the benefits of working in virtual reality instead of actual reality. The VR software company Nanome has a 21st century replacement for the ball and stick models that date from 1865 as well as software models that create 2D images of molecules on computer screens.

The VR platform has won over highly educated researchers who are skeptical of everything who at the same time have been waiting for decades for this technology to mature, according to Steve McCloskey, founder and CEO of Nanome.

“This gives a scientist a foundational understanding of the data they’re looking at and within seconds they have a completely different understanding,” he said. “They have orders of magnitude more information.”

He said the VR experience gives people who have been staring at a particular molecule for years a whole new perspective on atom-to-atom interactions.

“This gives researchers a full stereo understanding of these molecules with no more abstraction,” he said.

Andrey Kovalevsky, a senior R&D scientist in the neutron scattering division at Oak Ridge National Laboratory, said using the Nanome software is like stepping into a protein structure and seeing the world as the protein does, an experience more three-dimensional than any program can achieve on a computer monitor.

“One can almost feel how a small molecule ligand interacts with the target protein,” he said.

Kovalevsky uses the Nanome software for in-depth analysis of protein structures, designing structure-activity relationship studies and testing ideas for drug design.

“All this can be done with people inside a VR room with you as if we were looking and manipulating protein structures while being in a conference room together,” he said.

He said that the VR software allowed him to perform analyses that he only dreamed of previously.

“VR has helped two of our projects (inhibitors of SARS-CoV-2 main protease and antidotes for organophosphate-inhibited human acetylcholinesterase) to progress at a much faster pace than would be possible,” Kovalevsky said.

SEE: VR training expands to make collaborative education relevant to all workers and for all skills

Keita Fukanawa, COO of Nanome, sees the VR platform as a necessary complement to AI models and quantum computing algorithms that generate new drug prototypes.

“Even if you have an imaginary drug that an AI came up with out of nowhere, if you don’t understand the nuances of the 3D structure you would miss out on making the AI better,” he said.

Nanome raised more than $3 million in funding this year and recently announced its largest deployment to date with Roivant Discovery, the research division of the biopharmaceutical company Roivant Sciences. Roivant’s computational platform predicts the dynamic three-dimensional nature of protein structures, which are generated using quantum mechanics, molecular dynamics and machine learning techniques using a combination of in-house and cloud computing resources.

In addition to investing in AI and quantum computing, companies need to invest in training so that employees can understand and critically evaluate results and recommendations from algorithms, McClosky said.

“Spatial, immersive technology is critical for people being able to keep up with major tech breakthroughs,” he said.

Building molecules in virtual reality

McClosky has a degree in nanoengineering and started the company in 2016 with the idea to create a hands-on tool for working at nanoscale.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank is an open access digital data resource that contains 3D structure data for large biological molecules. PDB structures for proteins, DNA and RNA are available free for all data consumers. Nanome users load this PDB information into the software to start experimenting.

Researchers use Nanome’s MedChem Tool to select elements from the periodic table to design small molecules. Users can view a molecule from all angles and change its size from small enough to hold in a hand to large enough to stand underneath. The VR simulation also shows how the molecules move and interact with each other.

“You have one complicated 3D thing that is moving and interacting with another 3D thing, and VR really lends itself to this,” he said. “You can see the whole process, not just predict the structure with software.”

The platform also includes workflow and API integrations for molecule and project data, automated docking molecular dynamics and calculated properties.

Fukanawa said the company has three types of users:

  1. Individuals working alone in one-hour sessions (or until the headset’s battery dies)
  2. One to two people working together and then holding a weekly design review with other team member
  3. Group presentations ranging from five to 30 people in business and education settings

Users can record all activity in the workspace, including structures, menus and hand and arm movements for playback at a later time. Users can pause and interact with the structures during the playback, making it useful for asynchronous collaboration. McCloskey said that the Oakridge scientists also used the platform for remote work during the early months of the pandemic.

Nanome is useful for general chemistry engineering as well.

“We also have a university researcher who is doing battery research using our software,” he said.

The company has a public Slack channel for people interested in the tool. The software is free for personal use. There are single user licenses for research and classroom use as well as enterprise and cloud pricing tiers.