Release Notes, Version 2025.4.1
The following floe products have new versions for this release. Other packages are unchanged from the previous release.
AI Fold Floes Release Notes
v0.2.0 December 2025
General Notice
This package is built using
OpenEye-orionplatform==6.5.0,OpenEye-toolkits==2024.2.1, andOpenEye-Snowball==0.29.2.
Floe Updates
The Protein Sequence to AI Folded Structure Prediction Floe has been updated to run using the Boltz model. An optional MSA search prior to structure prediction has been added.
The Protein Sequence to AI Folded Structure Ligand Affinities Floe has been added, which takes an ensemble of input ligands that will be individually co-folded with the input sequences. Ligands with a higher affinity values will be ranked higher.
The MSA Align and Search Floe has been added, which runs an MMSeqs2 MSA search on input sequences.
The MSA Collection Setup from FASTA Floe has been added, which creates a FASTA collection that can be used with floes that perform an MSA search.
ChemInfo Hit ID Release Notes
v2.3.2 December 2025
General Notice
This package is built using
OpenEye-orionplatform==6.7.0,OpenEye-toolkits==2025.2.0, andOpenEye-Snowball==0.31.0.
Classic Lead Optimization Release Notes
v0.16.3 December 2025
General Notice
This package is built using
OpenEye-orionplatform==6.4.1,OpenEye-toolkits==2025.2.0, andOpenEye-Snowball==0.31.0.
Large Scale Floes Release Notes
4.3.1 December 2025
Fixes
The Gigadock Collection to Hi-res FastROCS Collection Floe has been adjusted to create smaller shards to address an out-of-memory error that could occur in the FastROCS Plus Floe.
The default name of the output design unit field has been changed from “Design Unit” to “designunit” in the Gigadock and Gigadock Warp Floes.
An issue has been fixed where the FastROCS Plus Floe would use FitTversky when RefTversky was specified by the user.
In the FastROCS Plus Floe parameter documentation, it has been clarified that color optimization is only supported with Tanimoto scoring, and that if RefTversky and FitTversky are selected, the optimization will be done with shape optimization and color scoring.
An out-of-memory error has been fixed in the FastROCS Plus Floe that occurred when the maximum number of rescore molecules (100M) was selected.
A rare issue has been fixed that caused some molecules to have Hetero Bemis Murcko cores with invalid valances in the FastROCS Plus Floe output.
Protein Modeling Release Notes
v1.1.0 December 2025
General Notice
This package is built using
OpenEye-orionplatform==6.7.0,OpenEye-toolkits==2025.2.0, andOpenEye-Snowball==0.31.0.
Small Molecule Modeling Release Notes
v2.3.3 December 2025
General Notice
This package is built using
OpenEye-orionplatform==6.5.1,OpenEye-toolkits==2025.2.0, andOpenEye-Snowball==0.30.1.
Floe Updates
Three new floes have been added in this release:
Clustering: 2D Scaffold (~25M compounds): This floe performs scaffold clustering on collections and files with inputs containing from 100K to millions of molecules.
Clustering: 2D Fingerprint, up to 100K compounds: This floe performs 2D-fingerprint-based DBSCAN, Hierarchical, and K-medoid clustering on inputs containing up to 100K molecules.
Clustering: 3D Shape/Color, ~10K compounds: This floe performs 3D ROCS based DBSCAN, Hierarchical, and K-medoid based clustering on inputs containing up to ~10K molecules.
The OMEGA - Conformer Generation for Macrocycles floe now fails molecule early if molecule does not have stereo specified.
The following floes have been deprecated:
DBSCAN 3D Similarity Clustering
DBSCAN 2D Similarity Clustering
Hierarchical 2D Similarity Clustering
Hierarchical 3D Similarity Clustering
K-Medoids 2D Similarity Clustering
K-Medoids 3D Similarity Clustering
Snowball Release Notes
v0.31.0 December 2025
General Notice
This package is built using
OpenEye-orionplatform=6.7.0,OpenEye-toolkits==2025.2.0,OpenEye-szmap==1.7.1.1, andOpenEye-szybki==2.8.0.1.
Cube Updates
The new MacroCycle Prep Cube has been added to check and prepare molecules for conformer generation with distance geometry using OMEGA.
The Flex-Protein Ligand Minimization Cube now properly updates the coordinates of the design unit components after optimization.
Version checking in Input PDB Codes for Spruce Cube has been removed to prevent failures due to endpoint changes at the RCSB.
Utility Floes Release Notes
v2.1.3 December 2025
This package is built using
OpenEye-orionplatform==6.5.1,OpenEye-toolkits==2025.2.0, andOpenEye-Snowball==0.31.0.