Elevating Molecular Visualization with MARA and Nanome 2.0

In the competitive landscape of molecular visualization and structure-based design, efficiency and clarity are non-negotiable. Tools like PyMOL and Maestro have long been cornerstones in the computational chemistry, medicinal chemistry, and protein engineering communities. However, integrating MARA and Nanome 2.0 into your workflows can unlock a new level of productivity, interactivity, and communication while preserving the visual fidelity and data integrity from these widely used platforms.

Switching tools often brings concerns about compatibility, data fidelity, and learning curves. MARA and Nanome 2.0 address this directly, ensuring that your docking results, multi-chain PDB files, and custom color schemes remain intact during the transition while maintaining an intuitive interface. Whether you’re analyzing multiple ligand poses from docking simulations or working with multi-chain complexes, these platforms carry over essential visual elements like respective atom and chain colors, annotations, and rendered surfaces. This seamless integration allows researchers to focus on their scientific insights rather than amending and troubleshooting representations.

We’re diving straight into how MARA and Nanome can effortlessly integrate with existing workflows. Imagine this: conducting docking experiments powered by MARA, performing quick visual analyses and setting your color schemes in PyMOL, and then transitioning into virtual reality with Nanome for an immersive understanding of the results. You can see the process from beginning to end here. While this entire workflow could be completed within MARA and Nanome 2.0 alone, the focus here is on how these tools enhance and complement the established processes already familiar to your laboratory.

Docking a Ligand in MARA

To generate docking data we will use MARA to dock a small molecule at a protein of interest. Simply asking MARA to prepare a protein file for docking and to find pockets is all that is needed to set up the protein for docking. A small molecule can then be easily docked at the protein by requesting to dock at a specific pocket.

Exporting from PyMOL

After setting up the visualization state of the docking results in PyMOL, simply save the system as a .pse file in a directory of your choice.

Loading a .pse in MARA

MARA makes it easy to import data from PyMOL and begin using tools in MARA on a system that has been set up in PyMOL. Users only need to drag and drop their .pse file directly into a MARA chat to get started. Once imported, the full potential of MARA tools are available to continue scientific investigations.

Sending a Structure from MARA to Nanome 2.0

One simple click is all that is needed to move a molecular representation from the MARA web interface to an investigation in virtual reality. Pro tip: MARA can be accessed through the web application native to the Meta Quest, thus allowing work saved in MARA to be sent to Nanome without ever leaving virtual reality!

Elevating Your Workflows with Nanome AI (MARA + Nanome 2.0)

The transition to MARA and Nanome 2.0 doesn’t mean abandoning established workflows—it means augmenting and empowering them. By keeping your PyMOL and Maestro representations intact and extending capabilities with cutting-edge immersive tools, you gain the freedom to focus on innovation rather than process. The ability to explore, design, and communicate molecular insights in a truly intuitive and collaborative environment is a game-changer. Check out the full video here. We look forward to seeing you in Nanome!