Release Notes, Version 2025.2.1

Release Highlights 2025.2

Small Molecule Discovery Suite Highlights

pKa Prediction Floes Package

The new pKa Prediction Floes Package predicts the dominant ionization states and pKas of small molecules. The ionization state of a drug candidate affects crucial physical properties including solubility, membrane permeability, target binding affinity, and ADMET. Therefore, using the correct ionization state for a given pH environment is very important to get accurate results from many computational methods, especially binding free energy calculations. The Generate Ionization States and Calculate LogD Floe predicts the dominant ionization state at a specified pH. The pKa Exploration Floe Floe provides a detailed report showing the titration curves and distributions of ionization states at different pH values.

Figure 1. The floe report identifies all ionizing groups and includes the titration curve, macrostate population curves, logD versus pH, microstate population curve, and micro- and macro-pKa reactions with tautomer ratios. This animated figure shows each aspect of the report and the changes of various features in relation to others. Note: to view the animation again, please refresh your browser after the animation has finished. Individual parts of the floe report can be found in the pKa Prediction Report within the pKa Exploration Floe tutorial.

Cryptic Pocket Detection Floes Package

Ligandability Assessment for Pocket Ranking and Representative Conformation Selection

Cryptic pockets are ranked by a ligandability prediction model which is trained and validated on a curated, nonredundant dataset consisting of diverse ligand-binding pockets. The unnormalized total score and normalized ligandability score, along with the significance score, are then computed for each pocket found during cryptic pocket detection.

Figure 2. The pocket ligandability score prediction.

Figure 3. The assessment of significance score (Bayes factor) for the normalized pocket ligandability score.

The new Ligandable Medoids Extraction Floe extracts an ensemble of ligandable medoid conformations for a selected pocket. A binding site view can be generated for pockets detected by probe binding analysis techniques after specifying “DUM” (the component representing xenon-occupancy grids for a pocket) as a ligand in the binding generation option.

Figure 4. The ligandability score and ranking for cryptic pocket predictions.

Improved Time and Cost Efficiency for Dynamic Probe Binding Analysis

The performance of the Dynamic Probe Binding Analysis Floe has significantly improved, now being ten times faster and five times lower in cost.

Detailed 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, and OpenEye-Snowball==0.30.0.

Floe Updates

• 3D QSAR Model: Builder

  • 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.

• 3D QSAR Model: Interpretation

  • 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.

• 3D QSAR Model: Validation

  • 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.

• 3D QSAR Model: Predictor

  • 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, and OpenEye-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.

Legacy Release Notes

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.

v0.2.7 March 2025

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

• The Cryptic Pockets Reporter Cube has a significantly lower memory requirement. This reduces 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, Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis Floes.

• Temporary checkpoint files and collection are deleted after the cryptic pocket analysis floes finish. This includes an auto-cleanup for the Automated Cryptic Pocket Detection with Probe Occupancy Analysis, Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis Floes.

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 Normal Mode-Guided Weighted Ensemble MD Simulation Floe generates and stores data in a V2 ShardCollection.

• The outputs have been changed from the Run a Normal Mode-Guided 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 Normal Mode-Guided Weighted Ensemble MD Simulation Floe now takes the collection generated by the Run a Normal Mode-Guided 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.

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).

Legacy Release Notes

v6.6.0 August 2025

General Notice

• This package was built using OpenEye-orionplatform==6.6.0 and OpenEye-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.

v6.3.2 January 2025

V6.3.2 is a rerelease of 6.3.1, with no change in content.

v6.3.1 September 2024

• A bug has been addressed in which SMILES data in an input file following CXSMILES data caused a parsing error.

• A bug has been addressed when exporting datasets to CSV files. All columns, or a subset thereof, can now be exported in cases when previously only Molecule and Molecule.Titled would have been exported.

v6.3.0 August 2024

• A bug has been addressed in which SMILES data in an input file following CXSMILES data caused a parsing error.

v6.2.0 June 2024

• Support for ShapeQuery (.sq) files has been added.

• Support for CXSMILES data has been added.

• Created collections have been defaulted to v1.

• A bug has been addressed by which some english language words (such as “BOTH”) could be interpreted as molecules.

v6.1.2 February 2024

• Columns can now be optionally ignored when exporting datasets.

v6.0.0 September 2023

• The version number has been synced with openeye-orionplatform.

• The Dataset to File Export ETL floes now preserve the Molecule Title when exporting to CSV files.

v2.3.0 July 2023

• This version increases the minimum versions of the requirements:

  • OpenEye-orionplatform==5.1.0

  • openeye-toolkits>=2022.2.2

v2.1.3 February 2023

• A floe for uploading large or small files from a URL has been added

v2.1.2 November 2022

• The orion-platform requirement has been updated to 4.5.2

v2.1.1 September 2022

• The orion-platform requirement has been updated to 4.4.1

• An issue where orionclient.types.Shard.download() could receive less data than expected has been fixed.

• An IOError will be raised and orionclient.types.Shard.download_to_file() will catch and retry.

v2.1.0 July 2022

• An issue with importing convert_path has been fixed.

• The etl-floe classifications has been updated to use the new PurePosixPath classifications

• The brief field has been added and the description field has been made more descriptive on all ETL floes.

• Requirement changes:

  • The Sphinx requirement has been updated to 3.5.4 and moved to requirements.txt.

  • The jinja2 requirement has been updated to 3.0.3.

  • The orion-platform requirement has been updated to 4.4.0.

  • The openeye-toolkits requirement has been updated to 2022.1.1.

  • The openeye-floe-pkg-tools requirement minimum version has been updated to 1.0.3.

• The etl-floe classifications has been updated to use the new PurePosixPath classifications.

• The “brief” field was added and the “description” field was made more descriptive on all ETL floes.

v2.0.2 February 2022

• Updated orion-platform to 4.3.0.

  • Converting datasets containing image data to csv now results in that field containing “<Image>”.

v2.0.1 December 2021

• The openeye-toolkits requirement has been updated to 2021.2.0

v2.0.0 November 2021

• The Collection Resize floe has been removed

v1.2.9 November 2021

• The orion-platform requirement has been updated to 4.2.5

v1.2.8 October 2021

• The orion-platform requirement has been updated to 4.2.4

  • A bug where the metadata of a collection was not being preserved when running the Collection Resize ETL floe has been fixed.

  • A required parameter collection_type in the ParallelCollectionResizeCube of the Collection Resize ETL floe has been promoted.

v1.2.7 October 2021

• orion-platform has been updated to 4.2.0

  • A failure caused by csv files containing no data for some columns has been fixed.

  • IUPAC names are no longer parsed, resulting in fewer column splits and ETL speedup.

  • A failure parsing lists of numbers has been fixed.

  • A bug in the naming of split columns has been fixed.

  • A failure when converting a record to OEB has been fixed. Fields with data that cannot be properly attached as generic data to a molecule are now skipped by default.

v1.2.6 June 2021

• The orion-platform requirement has been updated to 4.1.0 (mono-package)

• The OpenEye-toolkits requirement has been updated to 2021.1.1

• A regression in perceiving basic molecular properties for SMILES and CSV has been fixed.

v1.2.5 June 2021

• The orion-platform requirement has been updated to 4.0.0 (mono-package)

• Orion Platform >= 4.0.0 will not work with stacks older than 2021.1 due to usage of new APIs

• The OpenEye-toolkits requirement has been updated to 2020.2.4

• A new Converter, SmilesFileConverter, has been added.

• When converting CSV and SMILES format files to records, the original smiles are stored on output records.

• ETL floe documentation has been improved

v1.2.4 November 2020

• The orion-platform requirement has been updated to 3.1.0

  • BaseDatasetFieldAddOrReplaceCube has been added.

  • If no file extension is provided to DatasetWriterCube’s output file parameter, the file format is now OEDB.

  • OpenEye-floe==0.12.0

    • Adds support for versioning of WorkFloes.

    • Adds support for ordering of Parameters in the Orion UI.

    • An issue that resulted in Serial Cube Group initializer ports not incrementing the counts has been resolved.

  • OpenEye-drconvert==1.1.2

    • Bump OpenEye Toolkits

  • OpenEye-orionclient==3.1.0

    • Bump OpenEye Toolkits

  • OpenEye-datarecord==3.0.1

    • Bump OpenEye Toolkits

v1.2.3 August 2020

• orion-platform has been updated to 3.0.0

  • An issue with too frequent flushing in DatasetUpdaterCube has been fixed.

  • The DatasetAppenderCube now finalizes datasets.

  • OpenEye-datarecord==3.0.0

    • The implementation of datarecord has mostly moved to C++ in the toolkits.

    • A field type DesignUnit for storing OEDesignUnits has been added.

  • OpenEye-drconvert==1.1.0

    • Support for OEDesignUnit has been added

  • OpenEye-orionclient==3.0.0

    • Added OEDesignUnit support for dataset upload and download

    • Support for uploading OEDU files to datarecords has been added to upload()

    • orionclient.types.Datarecord.records now yields OEMolRecord

v1.2.2 April 2020

• orion-platform has been updated to 2.4.5

  • OpenEye-orionclient==2.6.3

    • The efficiency and reliability of ShardCollection.list_shards has been improved.

v1.2.1 March 2020

• orion-platform has been updated to 2.4.4

  • A bug in RecordsToCollectionCube has been fixed.

  • Improvement made to shard retries.

v1.2.0 February 2020

• The base OS image has been upgraded to Amazon Linux 2

• The environment has been upgraded to Python 3.8.1

• Package documentation has been added

• orion-platform has been updated to 2.4.2

  Improvements since 2.1.0 include:

  • Support for the OEZ format has been added to the following cubes:

    • CollectionResizeCube

    • CollectionToRecordsCube

    • RecordsToCollectionCube

  • orionplatform.cubes.files.RecordsToRecordFileConverter now uploads its files in parts reducing the disk usage

  • New parameters, which optionally enable metric collection for cubes have been added.

  • Sets lower bound on OpenEye-toolkits>=2019.10.2

  • A duplicate of output_tags in the DatasetWriterCube Options parameter group has been removed.

  • OpenEye-Drconvert==0.7.2

    • Support added for Float and Int vectors

    • Drconvert CLI now supports going from records to mols

v1.1.1 October 2019

• orion-platform 2.1.0

  • Improves reliability of uploading shards and writing shards of records

  • Adds limit parameter to ShardReaderCube to allow streaming only some shards from a collection.

v1.1.0 August 2019

• orion-platform 2.0.0

  • Improves reliability of collection floes

  • Updated version of drconvert (0.6.20) correctly handles conformer data

v1.0.0 July 2019

• orion-platform 1.0.2

v0.1.29 April 2019

• orion-platform 0.1.16

• Collection resize floe

v0.1.28 February 2019

Bugfixes

• drconvert 0.6.16

• No longer sets OEIsomericConfTest on file formats that are not mol2 or sdf

v0.1.27 February 2019

• Add Dataset Copy floe

v0.1.26 February 2019

• Orion Platform 0.1.14

  • openeye-drconvert>=0.6.15,<0.70

    • Performance improvements

Bugfixes

• Fixes ArchiveConverterCube

v0.1.25 January 2019

• Orion Platform 0.1.13

  • openeye-drconvert>=0.6.13,<0.70

    • Calls flush() before returning records from MolFileConverter

  • openeye-datarecord>=0.12.7,<0.13.0

    • Adds flush() to OERecord to write all cached values to bytes.

  • openeye-schemagen>=0.3.3,<0.4.0

    • Minor cleanup

v0.1.24 December 2018

• orion-platform 0.1.12

  Summary of changes relevant to ETL floes:

  • openeye-drconvert>=0.6.12,<0.7.0

    • Handle whitespace in SD data

  • openeye-orionclient>=0.6.10,<0.7.0

    • Makes Orion Client more robust to handling API changes

v0.1.23 November 2018

• orion-platform 0.1.11

v0.1.22 November 2018

• orion-platform 0.1.10

  Summary of changes relevant to ETL floes:

  • openeye-schemagen>=0.3.2,<0.4.0

  • survive SD data consisting of only whitespace

  • openeye-datarecord>=0.12.5,<0.13.0

  • add more testing for metadata; Serialize/deserialize round trips. ORION-6328

  • add Meta.Flags.Predicted metadata to datarecord. Minor cleanups. ORION-6328

v0.1.21 October 2018

• orion-platform 0.1.9

  Summary of changes relevant to ETL floes:

  • openeye-schemagen>=0.3.1,<0.4.0

    • delimiters back to ordering by descending priority

  • openeye-orionclient>=0.6.9,<0.7.0

    • 0.6.9

      • Adds headers to improve debugging capabilities

    • 0.6.8

      • Adds orionclient.exceptions.OrionTimeout exception that indicates that

        a request couldn’t be made to the specified Orion within the expected time

  • openeye-floe>=0.6.15,<0.7.0

    • 0.6.15

      • Fixes issue where parallel workers would incorrectly propagate failures when run in Orion

v0.1.20 October 2018

• add package uuid

v0.1.19 October 2018

• orion-platform 0.1.8 * fix memory leaks when reading dataset * improve robustness of collection handling

v0.1.18 September 2018

• orion-platform 0.1.7 orion-client fixes: * avoid writing too many records at once * fix issue retrieving records when sizes of records are not consistent

v0.1.17 September 2018

• orion-platform 0.1.6

v0.1.16 September 2018

• sync job system tags with backend/frontend

• bump orion-platform to 0.1.5 to force min versions

• remove default tag that appears to not be used

• Added continuation char BUGZID: ORION-6089

• Allowing non-SDData formats for etl export BUGZID: ORION-6089

v0.1.15 September 2018

• Needed to rev version because of Orion failing inspection due conflict with a previous failed upload of this version:

  “Workfloe Record Collection to Dataset with version:’0.1.14’ and uuid:’934d77a2-c1a1-421f-8daf-5b8ca6325fbf’ already exists for user with ID 1”

v0.1.14 September 2018

• Add package setup, tasks, tests, and release notes invoke upload-package puts package in S3 for devops to load onto stacks

• Update orion-platform requirement to 0.1.4, which pulls in toolkit, drconvert and related packages

• Add record collection floes

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, and OpenEye-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, and OpenEye-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, and OpenEye-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

v0.30.2 Sept 2025

Cube Updates

• A fix was added to the Input PDB Codes for Spruce Cube to prevent failure due to endpoint changes at the RCSB.

Utility Floes Release Notes

v2.1.2 September 2025

• This package is built using OpenEye-orionplatform==6.5.1, OpenEye-toolkits==2025.1.1, and OpenEye-Snowball==0.30.2.

Recent Release History

• Release 2025.1

• Release 2024.2.2

• Release 2024.2

• Release 2024.1

• Release 2023.2