Powerful New Integration: Nanome XR + OpenEye Tools for Drug Discovery
Nanome and Cadence have an exciting new integration that allows direct access to results calculated by the OpenEye platform directly into Nanome XR. Our integration of many of the OpenEye tools is just beginning and we are proud to announce that we have created tools to work with molecular search (Fast-ROCS), molecular dynamics simulations and other trajectories, and cryptic pocket evaluation.
Tools Currently Available to Work within Nanome XR and MARA
- FastROCS
- Conduct shape based searches at super fast speeds
- This exceptional speed enables you to perform highly accurate 3D shape similarity calculations on millions of molecules within seconds
- Offering a significant advantage over traditional 2D approaches.
- Iterate on interesting molecular search results directly in Nanome XR, then launch new queries from molecules drawn directly in a protein pocket
- Molecular Dynamics Simulations and other Trajectories
- MARA can now parse .h5 files created by Orion
- This allows users to download their data from Orion, then convert to .PDB and .XTC (using natural language or MARA workflows) to be parsed by Nanome XR.
- MARA further allows users to:
- Remove waters
- Center the trajectory
- Export specific frames as pdb
- Truncate a trajectory a specific section of frames
- Easily return information about the trajectory
- Cryptic pocket evaluation
- OpenEye's Cryptic Pocket Detection tools empowers users to thoroughly explore a protein's conformational space, potentially revealing one or more cryptic pockets.
- Readily locate sites that are rarely or never observed in experimental structures that can remain druggable
- Find novel opportunities for modulating the activity of a target protein
- Aids in crafting isoform-selective ligands
- Cryptics pockets are located using state-of-the-art enhanced sampling molecular dynamics simulations
- Plugins are available to directly load .OEDU files directly into Nanome to highlight the design units that encompass cryptic pockets.
How can this help our team innovate?
Scientific innovations require a thorough assessment of target protein scaffolds and the small molecules that bind therein. Coupling the computational toolsets provided by OpenEye with collaborative three-dimensional visualization empowered by Nanome, teams can leverage a new perspective on target molecules and their high quality hits to allow expedited forward progress. Bringing computational, medicinal, and synthetic chemists together with structural biologists, biochemists, and protein engineers in a shared three-dimensional environment creates the opportunity to see the unseen, predict better targets, and bring products to market while spending less time doing so.
How can I get my hands on these new integrations?
Do you already have access to the OpenEye tools?
- Contact sales@nanome.ai or use this calendar link to directly schedule an XR or MARA demo with the Nanome team at a time that works best for you and your team!
Written by:
Joseph A. Laureanti, PhD and Edgardo Leija from Nanome