How to Find Cryptic Pockets Using an Automated End-To-End Workflow (October 2024)
What you will learn: How to find cryptic pockets using an automated end-to-end workflow.
Estimated read time: 2 minutes.
Identifying cryptic pockets can significantly enhance drug discovery by revealing ligand binding sites that remain concealed in the static structures of target proteins.
The OpenEye Cryptic Pocket Detection package for Orion includes several floes designed to assist scientists in uncovering these hidden pockets. The package uses normal mode-driven enhanced sampling simulations alongside three physics-based methods for detection:
Exposon Analysis.
Dynamic Probe Binding Analysis.
Probe Occupancy Analysis.
Using probe occupancy analysis, scientists can leverage the Automated Cryptic Pocket Detection with Probe Occupancy Analysis Floe, which provides a comprehensive workflow for exploring cryptic pockets on target proteins.
The floe requires just one input: a single Spruce-prepared design unit (DU) of the target of interest, as shown below. In return, it produces DUs that include receptors for each identified pocket, which can be used for downstream applications.
To Learn More
Consult the basic tutorial documentation for the Cryptic Pocket Detection package.
Read the ChemRxiv Preprint on exploration of cryptic pockets.
Download the Science Brief on enhanced sampling of protein conformations for cryptic pocket detection.
Access the documentation page for the Cryptic Pocket Detection Floes package.
We are excited to share how these features can help accelerate the drug discovery process. Please contact us to schedule a personalized demo with one of our experts.