Since the release of Nanome, we’ve discussed our software with hundreds of individuals, including structural biologists, computational chemists, and medicinal chemists.

We’ve learned about their needs throughout the drug discovery process. In our experience so far, we often first shown our 3D molecular visualization software for virtual reality to structural biologists before being joined by their close colleagues.

A structural biologist studies the molecular structure and dynamics of biological macromolecules, such as proteins and nucleic acids, and how changes affect their function. Their goal is to visualize these structures in 3D in collaboration with other scientists. The idea is truly revolutionary.

This branch of molecular biology, biochemistry, and biophysics focuses on proteins comprised of amino acids comprised of RNA or DNA made up of nucleotides. Macromolecules carry out most of the functions of a cell.

Today, structural biologists can’t see the biomolecules on which they work even with the most advanced light microscopes. Structural biologists use measurements on vast numbers of identical molecules at the same time to determine a structure. Advances in software, through the use of virtual reality, could revolutionize this field of drug discovery.

The methods they use include mass spectrometry, macromolecular crystallography, proteolysis, nuclear magnetic resonance spectroscopy of proteins (NMR), electron paramagnetic resonance (EPR), cryo-electron microscopy (cryo-EM), multiangle light scattering, small angle scattering, ultrafast laser spectroscopy, dual-polarization interferometry, and circular dichroism.

Highly accurate physical molecular models, many of which are accessible from the Protein Data Bank (PDB) and materialized by Nanome’s software, aid the work of the structural biologist.

After the structural biologist, the drug development group is perhaps the most interested party in Nanome. This group consists of typically four to six people, who are often the structural biologist’s closest colleagues. They use Nanome to foster group collaboration.

This means that structural biologists and their closest colleagues are having their ‘a-ha’ moment when it comes to molecular visualization in 3D virtual reality. Fortunately, Nanome’s software adoption has been greatly accelerated due to the decreasing cost and increasing computational power of the underlying hardware.

Massive companies, such as Oculus’ (a popular VR headset company) parent Facebook, are committing significant resources towards producing and promoting VR use.

What features do the scientists want?

The users of our software, such as chemists, want to be able to zoom into the binding pocket of a molecule to procure information on proteins. They want to do this to gain a fuller understanding. They have general ideas for areas they think might form bond interactions or non-bonding interactions. Today, they will take a model they build by looking at it on a 2D screen, then they go to a 2D piece of paper or a whiteboard and they draw the chemical structures.

This 2D process creates a lot of junk data since a lot of the scientist’s hypotheses turn out wrong. If you take away the layers of abstraction and place the chemist right into the binding pocket in a 3D environment, they can make modifications directly in the binding pocket create a higher quality molecule in a more efficient manner.

Everyone has different DNA. Each individual has his or her own sequence. Each three base pairs in the DNA corresponds to one amino acid on the protein, which is called a codon.

If that codon of yours is different than the codon of the standard protein that they’re working with, then that means that I have a different amino acid, and depending on where that amino acid mutation is located on the protein, if it’s in the binding pocket or elsewhere, then maybe a different drug would work better.

Really understanding that could also mean the difference between life and death and better medicines.

Its why Nanome provides cutting edge tools for our clients: so they can discover better medicines at a faster rate.