Nanome uses VR to build molecules and make AI recommendations for reality testing


Chemists can manipulate molecules, observe proteins interacting and share their work with colleagues in the virtual reality platform.

The software company Nanome has developed a software platform that chemists and other researchers can use to build molecules in virtual reality and experiment with them.

Image: Nanome

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

The VR platform has convinced highly qualified researchers who are skeptical of everything and at the same time have waited decades for this technology to mature, according to Steve McCloskey, founder and CEO of Nanome.

“This gives a scientist a basic understanding of the data they are looking at and within seconds they have a completely different understanding,” he said. “You 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 without any further abstraction,” he said.

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

“You can almost feel a small molecule ligand interacting with the target protein,” he said.

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

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

With the VR software, he can carry out analyzes that he previously only dreamed of.

“VR has helped two of our projects (inhibitors of the SARS-CoV-2 major protease and antidotes for organophosphate-inhibited human acetylcholinesterase) advance much faster than they could,” said Kovalevsky.

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

“Even if you have an imaginary drug that AI evolved from scratch, you’d miss out on making the AI ​​better if you didn’t understand the nuances of 3D structure,” he said.

Nanome raised more than $ 3 million in funding this year and recently announced its largest ever commitment to Roivant Discovery, the research division of biopharmaceutical company Roivant Sciences. Roivant’s computing platform predicts the dynamic three-dimensional nature of protein structures 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 must also invest in training so that employees can understand and critically evaluate results and recommendations from algorithms, McClosky said.

“Spatial, immersive technology is critical to enabling people to keep up with major technological breakthroughs,” he said.

Build molecules in virtual reality

McClosky has a degree in nano-engineering and founded the company in 2016 with the idea of ​​creating a practical tool for working on the nano-scale.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank is an open access digital data source that contains 3D structural data for large biological molecules. PDB structures for proteins, DNA and RNA are available to all data consumers free of charge. 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 develop small molecules. Users can view a molecule from all angles and change its size from small enough to hold in their hand to large enough to stand under. The VR simulation also shows how the molecules move and interact with each other.

“You have a complicated 3-D thing that moves and interacts with another 3-D thing, and VR is really good for that,” 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 who work alone in one-hour sessions (or until the headset runs out of battery)
  2. One or two people work together and then do a weekly design review with other team members
  3. Group presentations of five to 30 people in companies and educational institutions

Users can record all activity in the work area, including structures, menus, and hand and arm movements, for later review. Users can pause and interact with the structures during playback, which makes them useful for asynchronous collaboration. McCloskey said Oakridge scientists also used the platform to work remotely during the first few months of the pandemic.

Nanome is also useful in general chemical engineering.

“We also have a university researcher who does battery research with 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 teaching purposes, as well as enterprise and cloud pricing tiers.

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