Release Notes

v0.2.5 September 2024

General Notice

• This package is built using OEToolkits 2024.1.1, Orion Platform 6.1.2, and Snowball 0.28.0, Orion Molecular Dynamics (MD) Core 2.4.2.

Minor Changes

• A fix has been made to allow analysis of protein structures with protonated histidine residue names (HIE, HID and HIP).

• An issue with display of pocket residues in the cryptic pocket analysis floe report has been fixed. It now displays the pocket residues when the protein chain IDs do not begin with “A” or when the protein chain IDs do not follow the alphabetical order.

v0.2.4 July 2024

General Notice

• This package is built using OEToolkits 2024.1.1, Orion Platform 6.1.2, and Snowball 0.28.0, Orion Molecular Dynamics (MD) Core 2.4.2.

Minor Changes

• A correction has been made in the axis of the 2D free energy projection on the normal modes.

• A default value for mutual information cut-off for pocket detection using the Dynamic Probe Binding Analysis and Exposon Analysis Floes is set to 0.00. This parameter is also now exposed to users under Cube Parameters.

• Faster receptor creation in the Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis Floes makes them more time efficient.

• The documentation now includes an FAQ section.

v0.2.2 April 2024

General Notice

• This package is built using OEToolkits 2023.2.3, Orion Platform 6.1.2, and Snowball 0.27.1.

Note

There is a known incompatibility between datasets created by previous versions of Cryptic Pocket Detection and datasets used by this version. If you need assistance with this issue, please contact Support@eyesopen.com.

Major Changes

• The Automated Cryptic Pocket Detection with Probe Occupancy Analysis Floe is introduced for automated, end-to-end workflows for cryptic pocket detection with probe occupancy analysis using an input design unit prepared using Spruce.

• Three advanced Floes (Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis) automate the cryptic pocket analysis process by integrating analysis of weighted ensemble protein sampling data, iterative clustering, cryptic pocket detection, and receptor creation.

• Weighted ensemble protein sampling data storage has been significantly refactored, which reduces the overall size by half and supports faster data find and read.

• Two new options have been added, Maximum Number of Selected Modes and Mode Filtering Property, in the Calculate Normal Modes Floe that allow for automatic rank and select modes based on specific mode properties. This feature is turned On by default in the Automated Cryptic Pocket Detection with Probe Occupancy Analysis Floe.

Minor Changes

• In addition to the Automated Cryptic Pocket Detection with Probe Occupancy Analysis Floe, individual sub-floes starting from the Solvate and Equilibrate Target Protein Floe to three cryptic pocket analysis Floes (Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis) can be sequentially run for protein sampling and cryptic pocket analysis.

• Now the Run a Weighted Ensemble MD Simulation Floe generates and stores data in a V2 ShardCollection.

• The outputs have been changed from the Run a Weighted Ensemble MD Simulation Floe. Now the output dataset contains multiple records (one record per iteration) and only contains summary statistics for the simulation. All simulation data (e.g., weighted ensemble data, MD trajectories, simulation files) are stored in the output shard collection. The collection is now self-contained and required as input for downstream analysis Floes.

• The Subsystem Selection String option has been substituted with Environment Selection String in the Calculate Normal Modes Floe for ease of use. Now the system-environment framework is enabled by default in the Floe.

• The Continue a Weighted Ensemble MD Simulation Floe now takes the collection generated by the Run a Weighted Ensemble MD Simulation Floe as the input to resume the weighted ensemble protein sampling simulation.

v0.1.2 September 2023

General Notice

• This package is built using OEToolkits 2023.1.0, Orion Platform 5.1.1, and Snowball 0.26.0.

Minor Changes

• Fixes an issue related to “select string” parameter format in the Calculate Normal Modes floe.

• Enables support for non-canonical amino acids in the Solvate and Equilibrate Target Protein floe.

• A minor typographical correction in documentation for the Calculate Normal Modes floe.

v0.1.0 July 2023

General Notice

• This is the first release of OpenEye Cryptic Pocket Detection Floes.

• This package is built using OEToolkits 2023.1.0, Orion Platform 5.1.0, and Snowball 0.26.0.