BIOMOLECULAR MODELING

Protein Cryptic Pocket Detection

The identification and exploitation of binding sites in protein structures often represents a pivotal step in designing effective therapeutics. Sites that are rarely or never observed in experimental structures, yet remain druggable, are referred to as cryptic pockets. These pockets offer novel opportunities for modulating the activity of a target protein and are particularly valuable in crafting isoform-selective ligands when the structure of the substrate-binding site remains consistent across different variants of the target protein.

Through the use of state-of-the-art enhanced sampling molecular dynamics simulations, OpenEye's Cryptic Pocket Detection tools empowers users to thoroughly explore a protein's conformational space, potentially revealing one or more cryptic pockets. Customized visual and quantitative analysis of the results can yield valuable insights into the presence and potential druggability of these pockets.

Cryptic Pocket CAK Exposon Analysis Static Image

Cryptic Pocket Detection reveals an additional pocket in CAK using Exposon analysis.

Features

Performance. Fast and efficient computation with Weighted Ensemble MD and Probe Finding for efficient exploration of potential binding sites
Rank Pockets. Available ligandability prediction model helps rank cryptic pockets and guide conformation selection, streamlining its use for users.
Turn-key. Automated single step end-to-end workflows
Flexible. Handles single and mixed solvent simulations
Versatile. Multiple pocket detection methods are provided

Uncover hidden features in protein structures

Transitioning from static structures to dynamic insights is a critical aspect of computational chemistry.

OpenEye provides users with automated workflows to explore hidden putative ligand binding sites for challenging protein targets. Users can:

Prepare and execute Weighted Ensemble (WE) Molecular Dynamics (MD) simulations in a single or mixed solvent.
Conduct pocket detection analysis to identify potential cryptic pocket sites.

With OpenEye's Weighted Ensemble MD and Cryptic Pocket Detection on the Orion® Molecular Design Platform, scientists can run calculations across hundreds or even thousands of GPUs in the cloud, saving valuable discovery time.

Image shows an example of using dynamic probe binding analysis method to identify cryptic pockets in K-Ras protein.

OpenEye's Cryptic Pocket workflow provides users with multiple pocket detection methods.

OpenEye’s tools for detecting these cryptic pockets helps you uncover alternative binding sites that are not apparent from the protein's primary function or known active sites. The identification of such cryptic pockets can lead to the discovery of new therapeutic opportunities and the design of novel drugs.

OpenEye’s Cryptic Pocket Detection comes with fully automated workflows to simplify your calculations. Users can access an end-to-end workflow that automated these steps:

Solvate and equilibrate target proteins (in single or mixed solvent)
Calculate normal modes
Perform a Weighted Ensemble MD simulation
Run cryptic pocket detection search

It's important to note that no single pocket detection method is foolproof, and a combination of different approaches may be used to increase the accuracy and reliability of detecting cryptic pockets in proteins. Hence, OpenEye provides three independent methods for your cryptic pocket detection:

Exposon Analysis (Solvent accessible surface area change, single solvent only)
CoSolvent Binding Free Energy Analysis (Probe-map analysis)
Cooperative CoSolvent Binding Analysis (Dynamic probe binding analysis)

With the OpenEye’s Cryptic Pocket method, users can perform protein sampling simulations that are solvated in water (single solvent) and/or are solvated in water and xenon (mixed solvent)

OpenEye’s Cryptic Pocket method offers the advantage of using water and xenon (mixed solvent) in the protein sampling. Using xenon as a probe offers advantages including:

Xenon is a non-selective binder to hydrophobic sites¹
Xenon has a fast diffusion rate²
Xenon localization has been observed in pocket composed of hydrophobic and hydrophilic residues¹

Schiltz M et al., Structure. 1995, 3, 309
Zhao Z et al., Biophys J. 2022 Dec 6;121(23):4635

OpenEye’s Cryptic Pocket Detection offers a cost-effective approach to uncover binding sites. Compute costs may vary depending on the protein size, but the runs typically average a few hundred dollars.

Learn More

OpenEye's Cryptic Pocket Detection can help you minimize the risk of off-target activity and undesired side effects, and thus save costs by reducing failure rates.

Download OpenEye Science Brief on Enhanced Sampling of Protein Conformations for Cryptic Pocket Detection

Watch OpenEye's recorded webinar from August 2025 for Dr. David LeBard's presentation on ligandability and Cryptic Pockets for Drug Discovery.

References

Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling. Porter, J. R.; Moeder K. E.; Sibbald C. A.; Zimmerman M. I.; Hart K. M.; Greenberg M. J.; Bowman G. R., Biophys J. 2019, 116(5), 818-830. doi: 10.1016/j.bpj.2018.11.3144. Epub 2019 Jan 25. PMID: 30744991; PMCID: PMC6400826.
Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRAS ^G12D. Vithani N, Zhang S, Thompson JP, Patel LA, Demidov A, Xia J, Balaeff A, Mentes A, Arnautova YA, Kohlmann A, Lawson JD, Nicholls A, Skillman AG, LeBard DN. J Chem Inf Model. 2024 Nov 11;64(21):8258-8273. doi: 10.1021/acs.jcim.4c01435. Epub 2024 Oct 17. PMID: 39419500; PMCID: PMC11558672.