Cryptic Pocket Detection Floes

v0.3.1 August 2025

General Notice

• This package is built using OpenEye-toolkits==2025.1.0, OpenEye-orionplatform==-6.4.1, OpenEye-Snowball==0.30.0, and OpenEye-orionmdcore==2.5.4.

Minor Changes

• The Automated Cryptic Pocket Detection with Probe Occupancy Analysis, Combined Probe Binding Site Analysis, Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis Floes will finish with the job status “Success” if no cryptic pockets are detected for a given target instead of a “Failed” completion. A Failure Report will be generated listing the potential reasons and next recommendations when no pockets are detected for a target.

• If users provide optional Important Residues input while running the Automated Cryptic Pocket Detection with Probe Occupancy Analysis, Combined Probe Binding Site Analysis, Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis Floes, the center-of-mass distance between the user-defined Important Residues and Pocket Residues will be reported for each pocket in the Pocket Receptors output dataset generated by these floes.

Major Changes

• The Filter Trajectory Features Data Cube (previously named Preprocess Trajectory Analysis Data) has a seven-to-tenfold lower memory requirement. The Curate Cryptic Pockets Cube (previously named Cryptic Pockets Reporter Cube) has more than a twofold lower memory requirement. Collectively, these changes reduce the chances of failure due to memory error associated with cryptic pocket floe report generation while running the Automated Cryptic Pocket Detection with Probe Occupancy Analysis, Combined Probe Binding Site Analysis, Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis Floes.

• The Dynamic Probe Binding Analysis is more than twelvefold faster in this version. The run cost for this floe is now expected to be fivefold less than the previous version.

• A new floe, Combined Probe Binding Site Analysis, that combines Probe Occupancy Analysis and Dynamic Probe Binding Analysis has been introduced. Running this floe eliminates the need to separately run the Probe Occupancy Analysis and Dynamic Probe Binding Analysis Floes for cryptic pocket detection.

• A new OEligandability-score based pocket ranking has been introduced. For each pocket reported by the Automated Cryptic Pocket Detection with Probe Occupancy Analysis, Combined Probe Binding Site Analysis, Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis Floes, the total ligandabilty score; the ligandability score normalized by total surface points as well as by receptor volume; and the ligandability significance score will be reported in the Pocket Receptors output dataset.