Release Notes, Version 2025.3.1
Cryptic Pocket Detection Floes
v0.3.2 September 2025
General Notice
This package is built using
OpenEye-toolkits==2025.1.1,OpenEye-orionplatform==6.7.0,OpenEye-Snowball==0.30.0, andOpenEye-orionmdcore==2.5.4.
Minor Changes
Floes now assign missing atomic radii directly to make them more robust to a variety of protein preparation methods.
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 have been improved to use the normalized ligandability score in their pocket filtration.
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 now correctly output multiple holo design units superposed with the pocket receptors.
The Run a Normal Mode-Guided Weighted Ensemble MD Simulation Floe was previously titled the Run a Weighted Ensemble MD Simulation Floe. Similarly, the Continue a Normal Mode-Guided Weighted Ensemble MD Simulation Floe was previously titled the Continue a Weighted Ensemble MD Simulation Floe. These changes have been made to specify that these floes use protein normal modes as progress coordinates for driving the weighted ensemble simulations.
Format Conversion (ETL) Floes
v6.7.0 September 2025
General Notice
This package is built using
OpenEye-orionplatform==6.7.0andOpenEye-toolkits==2025.1.1.
Functional Changes
There is a new floe for archiving files and datasets.
Machine Learning Model Building Floes
v1.0.2 September 2025
This package is built using
OpenEye-orionplatform==6.7.0,OpenEye-toolkits==2025.1.1,OpenEye-Snowball==0.29.2, andOpenEye-floereport==6.7.0.
Feature Updates
New floes have been added to allow for model building and property prediction using Graph Convolutional Neural Network (GCNN) models. GCNNs can learn directly from the molecular graph using atom and bond features from OpenEye toolkits rather than features derived from the molecule (e.g., fingerprints), resulting in fewer parameters for the model to learn. GCNNs are also not limited to interaction radii from complex structures, therefore building more generalizable models.
A new parameter, Graph Feature Vector Generation, has been added to the Data Processing of Small Molecule for ML Model Building Floe. This parameter builds graph feature tensors and outputs a collection with graph nodes and edge features that will be used as input for the GCNN model building floe.
There is an informative new chapter on How to Build Optimal Property-Predicting Graph Convolutional Neural Network Machine Learning Models by Tweaking Neural Network Architecture.
New Floes
These floes have been introduced and described in the new ML Build and Predict: Optimal Property-Predicting Graph Convolutional Neural Network Model tutorial:
Molecular Dynamics Affinity
v 6.5.7 September 2025
General Notice
This version pins
orionmdcore==2.5.3.1, where temporary resources are deleted immediately after use.The NES chimera construction has been improved to avoid cube failures during ring fusion involving a cyclopropyl group.
Molecular Dynamics Core Package
v2.5.5 September 2025
General Notice
This package is built using
openeye-orionplatform >=5.1.1, <7,openeye-snowball >=0.26.0,openeye-toolkits >=2023.2.3,openff-toolkit >=0.14.4, <0.15, andparmed ==3.4.4.
Updates
Legacy cubes and API points have been removed to upgrade old data formats.
Temporary resources are now deleted immediately after use.
Bug Fixes
A bug has been fixed that could cause Gromacs to crash when multiple water residue names were present.
pKa Prediction Floes
v0.2.0 September 2025
General Notice
This package is built using
OpenEye-toolkits==2025.1.1,OpenEye-orionplatform==6.7.0, andOpenEye-Snowball==0.30.0.
Feature Updates
The resonance has been fixed in cases where unfavorable structures were generated due to enumerating protonated and deprotonated states of atoms within or around aromatic rings.
The LogD calculation has been improved.
The UI/UX experience in workfloe Job Forms has been improved.
Structural Biology Floes
v0.1.2 September 2025
General Notice
This package is built using
OpenEye-toolkits==2025.1.1,OpenEye-orionplatform==6.7.0,OpenEye-Snowball==0.30.0, andOpenEye-orionmdcore==2.5.4.This is the first release of the OpenEye Structural Biology Floes package.