Release Notes, Version 2025.2.1
3D QSAR Models
v1.2.0 August 2025
General Notice
This package is built using
OpenEye-orionplatform==6.5.1,OpenEye-toolkits==2025.1.0, andOpenEye-Snowball==0.30.0.
Floe Updates
The floe now allows users to select a set of 3D models to build.
Two new 3D models, ROCS-GPR-NO-2D and EON-GPR-NO-2D, have been added. Unlike ROCS-GPR and EON-GPR, these two GPR models only use 3D Tanimoto as descriptors.
The floe now accepts kcal/mol and kJ/mol as potency units.
The default cross-validation method has been switched from “leave one out” to “random” to accommodate for a larger training set.
The option Include 2D in COMBO has been added to allow the user to decide whether to incorporate 2D-GPR into final model predictions.
A new parameter section, Cube Memory Parameters, has been added to allow users to increase the memory of some cubes for relatively large training sets to avoid cube memory errors.
Grids corresponding to color atom probes have been added to the output dataset, along with contour values used for generating high and low surfaces.
The domain grid has been deleted from the output dataset.
The Generate ROCS Query parameter has been removed. ROCS query output will be generated by default along with ROCS-kPLS model interpretation.
A new parameter, Selected Models, has been added, allowing for the selection of kPLS models to interpret.
A new parameter, Percentage for Surface Contour Values, has been added to give the user more flexibility to choose contour values for high and low surfaces.
A new parameter section, Cube Memory Parameters, has been added to allow users to increase the memory of some cubes for relatively large training sets to avoid cube memory errors.
A new parameter section, Cube Memory Parameters, has been added to allow users to increase the memory of some cubes for relatively large training sets to avoid cube memory errors.
A new parameter section, Cube Memory Parameters, has been added to allow users to increase the memory of some cubes for relatively large training sets to avoid cube memory errors.
Classic Lead Optimization
v0.16.2 August 2025
General Notice
This package is built using
OpenEye-orionplatform==6.4.1,OpenEye-toolkits==2025.1.1, andOpenEye-Snowball==0.30.1.
Floe Updates
The default memory for the single-receptor Posit Cube has been increased to 4*1.8*1024 in the POSIT - Ligand Guided Small Molecule Posing Floe.
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, andOpenEye-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.
Generative Design Floes
New Tutorial August 2025
A new tutorial was added to the documentation: Tutorial: Library Enumeration for Hit Identification.
Software features are the same as with v2.4.1 (January 2025).
Format Conversion (ETL) Floes
v6.6.0 August 2025
General Notice
This package was built using
OpenEye-orionplatform==6.6.0andOpenEye-toolkits==2024.1.1.
Functional Changes
The records_per_shard parameter on the ParallelRecordsToCollectionCube cube has been promoted in the Dataset to Collection Export ETL floe.
pKa Prediction Floes
v0.1.0 August 2025
General Notice
This package is built using
OpenEye-orionplatform==6.5.1,OpenEye-toolkits==2025.1.0, andOpenEye-Snowball==0.30.0.This is the first release of OpenEye Small Molecule pKa Prediction Floes package.
Protein Modeling Floes
v1.0.2 August 2025
General Notice
This package is built using
OpenEye-orionplatform==6.6.0,OpenEye-toolkits==2025.1.0, andOpenEye-Snowball==0.30.0.
Small Molecule Modeling
v2.1.1 August 2025
General Notice
This package is built using
OpenEye-orionplatform==6.5.1,OpenEye-toolkits==2025.1.0, andOpenEye-Snowball==0.30.0.
Floe Updates
The OEDocking - Dock into an Active Site for Virtual Screening Floe has the following updates:
There is an option to fail optimized poses for excessive bending of aromatic rings in the Refined and STMD quality options.
The AUTO docking mode now uses FRED or HYBRID for docking based on the similarity of the molecule to the bound ligand.
FRED is used if the receptor is apo, or if the molecule has low similarity to the bound ligand.
HYBRID is used if the receptor is holo, and if the molecule has high similarity to the bound ligand.
You can now use the same protein mask in the Docking, Optimization, and Check Clashes Cubes.
These changes have been made in the STMD mode. You can now:
Generate 50 poses using exhaustive docking with FRED.
Perform pose clustering before optimization (in addition to one after optimization) using the ChemGauss4 Score for ranking the pose before optimization, and an RMS threshold of 1.0 for deduplication.
Perform deduplication of a pose as it is, without doing any overlay.
The SZYBKI - Ligand Minimization in a Rigid Active Site Floe and SZYBKI - Ligand Minimization in a Flexible Active Site Floe have a new parameter, bent_ring_check, to set whether or not to fail the optimization when there is excessive deviation from planarity in aromatic rings.
Snowball
v0.30.1 August 2025
General Notice
This package is built using
OpenEye-orionplatform=6.6.0,OpenEye-toolkits==2025.1.0,OpenEye-szmap==1.7.1.1, andOpenEye-szybki==2.8.0.1.
New Cubes
The new Docking Method Selector (Single Receptor) Cube has been added to select the docking method (FRED or Hybrid) based on similarity to the bound ligand and to emit the record to the corresponding port.
Cube Updates
OMEGA cubes now have the option to use Thompson sampling.
The Omega Conformation Cube now has an option to turn on Thompson sampling for OMEGA torsion driving.
A new OMEGA mode, ROCS-TS, generates conformers suitable for ROCS calculations using Thompson sampling.
The Generate 3D Cube now uses OEConformerBuilder, a Thompson sampling based method, to generate 3D structures for input molecules.
The Slice Ensemble Cube has the option to perform slice ensembles with or without RMS overlay.
The following cubes all use a protein mask from the receptor by default:
The following cubes have the option of whether or not to fail optimization for excessive bending of aromatic rings:
The Check clashes (Individual) Cube and Check clashes (Series) Cube have the option to choose the types of clashes to ignore: None, Hydrogen, or Any.
The Check Optimized Pose Cube emits a clashed status of each pose. It also emits a failure log if all poses are clashing or if they have deviated too far after optimization. By default, a hydrogen clash is allowed by this cube.
The Fixed-Protein Ligand Minimization Individual Cube and Fixed-Protein Ligand Minimization Series Cube emit the RMSD of optimized poses.
The Fixed-Protein Ligand Minimization Series Cube only sends the record to the failure port if none of the conformers of the molecule could be optimized.
The Brood DB Reader Cube can now handle tarballs created on macOS containing AppleDouble files (with the prefix ‘._’).
The Exhaustive Docking (Single Receptor) Cube has a new option to not fail when an apo receptor is passed for
HYBRIDmode, and switch to useFREDmode instead.
Utility Floes
v2.1.1 August 2025
General Notice
This package is built using
OpenEye-orionplatform==6.5.1,OpenEye-toolkits==2025.1.1, andOpenEye-Snowball==0.30.0.
Floe Updates
The following improvement has been made to the OMEGA - 3D Conformer Ensemble Generation Floe: A new Conformer Generation Mode option, ROCS-TS, has been added which uses Thompson Sampling to generate conformers suitable for ROCS calculations.