2025.2
Release Highlights 2025.2
Small Molecule Discovery Suite Highlights
pKa Prediction Floes Package
Cryptic Pocket Detection Floes Package
Release Notes, Version 2025.2.1
3D QSAR Models
v1.2.0 August 2025
General Notice
Floe Updates
Classic Lead Optimization
v0.16.2 August 2025
General Notice
Floe Updates
Cryptic Pocket Detection Floes
v0.3.1 August 2025
General Notice
Minor Changes
Major Changes
Generative Design Floes
New Tutorial August 2025
Format Conversion (ETL) Floes
v6.6.0 August 2025
General Notice
Functional Changes
pKa Prediction Floes
v0.1.0 August 2025
General Notice
Protein Modeling Floes
v1.0.2 August 2025
General Notice
Small Molecule Modeling
v2.1.1 August 2025
General Notice
Floe Updates
Snowball
v0.30.1 August 2025
General Notice
New Cubes
Cube Updates
Utility Floes
v2.1.1 August 2025
General Notice
Floe Updates
Recent Release History
Small Molecule Discovery Suite
Introduction
Module-Level Tutorials for the Small Molecule Discovery Suite
Target Exploration Module
Target Exploration Overview Tutorial
Hit Identification Module
Hit Identification Overview Tutorial
Lead Optimization Module
Lead Optimization Overview Tutorial
Target Exploration Module
Target Exploration Overview Tutorial
Cryptic Pocket Detection
Introduction
Tutorials
OpenEye Cryptic Pocket Detection Floes - Documentation
Cryptic Pocket Detection Floes
Legacy Release Notes
Bibliography
Protein Modeling Floes
Introduction
Tutorials
Protein Modeling Floes - Documentation
Protein Modeling Floes
Protein Modeling Release Notes
AI Fold Floes
AI Fold Floes - Documentation
Release Notes
Format Conversion
Orion ETL Floes - Documentation
Format Conversion (ETL) Floes
Legacy Release Notes
Utility Floes
Introduction
Tutorials
How To Guides
Utility Floes - Documentation
Utility Floes
Utility Floes Release Notes
Historical Release Notes
Hit Identification Module
Hit Identification Overview Tutorial
ChemInfo Hit ID Floes
Introduction
OpenEye ChemInfo Hit ID Floes - Documentation
ChemInfo Hit ID Release Notes
ChemInfo Hit ID Release Notes
Generative Design Hit-to-Lead Floes
Tutorials
Floe Reference Documentation
Release Notes
Legacy Release Notes
Large Scale Floes
Tutorials
How-to Guides
Explanations
Floe Reference Documentation
Release Notes
Legacy Release Notes
Large Scale Floes Hit-to-Lead
Explanations
Floe Reference Documentation
Release Notes
Legacy Release Notes
pKa Prediction Floes
Introduction
Tutorials
Frequently Asked Questions
Small Molecule pKa Prediction Floes - Documentation
pKa Prediction Floes
Protein Modeling Floes
Introduction
Tutorials
Protein Modeling Floes - Documentation
Protein Modeling Floes
Protein Modeling Release Notes
Small Molecule Modeling Floes
Introduction
Tutorials
Small Molecule Modeling - Documentation
Small Molecule Modeling
Small Molecule Modeling Release Notes
AI Fold Floes
AI Fold Floes - Documentation
Release Notes
Format Conversion
Orion ETL Floes - Documentation
Format Conversion (ETL) Floes
Legacy Release Notes
Utility Floes
Introduction
Tutorials
How To Guides
Utility Floes - Documentation
Utility Floes
Utility Floes Release Notes
Historical Release Notes
Lead Optimization Module
Lead Optimization Overview Tutorial
3D QSAR Modeling Floes
Introduction
Theory
Tutorials
OpenEye 3D QSAR Models - Floe Documentation
Benchmark Results
3D QSAR Models
Legacy Release Notes
Bibliography
Classic Lead Optimization Floes
Introduction
Tutorials
Classic Lead Opt Floes - Documentation
Classic Lead Optimization
Classic Lead Optimization Release Notes
Generative Design Hit-to-Lead Floes
Tutorials
Floe Reference Documentation
Release Notes
Legacy Release Notes
Generative Design Lead Optimization Floes
Tutorials
Floe Reference Documentation
Release Notes
Legacy Release Notes
Large Scale Floes Hit-to-Lead
Explanations
Floe Reference Documentation
Release Notes
Legacy Release Notes
Machine Learning Model Building Floes
Introduction
Tutorials
Tutorials to Build Machine Learning Models
Tutorials to Predict Molecules Based on Trained Machine Learning Models
How-To Guides
Floe Reference Documentation
Theory
FAQs
Bibliography
Release Notes
Legacy Release Notes
Molecular Dynamics Affinity Package
Introduction
How-To Guide and Tutorials
MD Affinity Floes - Documentation
Molecular Dynamics Affinity Release Notes
Legacy Release Notes
Permeability Floes
Tutorials
OpenEye Permeability Floes - Documentation
Release Notes
pKa Prediction Floes
Introduction
Tutorials
Frequently Asked Questions
Small Molecule pKa Prediction Floes - Documentation
pKa Prediction Floes
Protein Modeling Floes
Introduction
Tutorials
Protein Modeling Floes - Documentation
Protein Modeling Floes
Protein Modeling Release Notes
Quantum Mechanics Psi4 Floes
Psi4 QM Floes - Documentation
How-To Guides
Frequently Asked Questions
Release Notes
Bibliography
Small Molecule Modeling Floes
Introduction
Tutorials
Small Molecule Modeling - Documentation
Small Molecule Modeling
Small Molecule Modeling Release Notes
AI Fold Floes
AI Fold Floes - Documentation
Release Notes
Format Conversion
Orion ETL Floes - Documentation
Format Conversion (ETL) Floes
Legacy Release Notes
Utility Floes
Introduction
Tutorials
How To Guides
Utility Floes - Documentation
Utility Floes
Utility Floes Release Notes
Historical Release Notes
Antibody Discovery Suite
3D Antibody Modeling Package
3D Antibody Modeling Tutorial
Floes Used in This Tutorial
Importing Sequences
Antibody Model Generation
Modeling Results
Antibody MD Simulations Tutorial
Antibody Molecular Dynamics Simulations
Understanding Antibody Surfaces and Annotations
Surface Patches
Structure Annotations
Antibody SiteHopper-based Clustering Tutorial
Result Analysis
OpenEye 3D Antibody Modeling - Documentation
Antibody CDR Loop Ensemble Generation
Antibody Experimental Structure Prep
Antibody MD Simulations with Conformational Analysis
Antibody Mutate Residue(s)
Antibody SiteHopper-based Clustering
Antibody Structure Relaxation
Antibody Subset System
Antibody Surface Patch Generation
Antibody-Antigen Interface Ala-scanning
Export Dataset to Fasta
Humanize Fv Antibodies
Import Antibody FASTA Files
Renumber and Restyle Antibody
Sequences to 3D Models for Fv Antibodies
Sequences to 3D Models for Nanobodies
Release Notes
v0.1.8 July 2024
v0.1.3 April 2024
Bibliography
AbXtract™ - NGS Antibody Discovery
Introduction to AbXtract
Tutorials
Tutorial 1: NGS Pipeline with Custom Interactive Selection (PacBio), In-Vitro Library
Tutorial 2: NGS Pipeline with Automated Top Lead Selection (PacBio), In-Vitro Library
Tutorial 3: NGS and Sanger Pipeline with Automated Top Lead Selection (PacBio), In-Vitro Library
Tutorial 4: NGS and Sanger Pipeline with Automated Top Lead Selection (Illumina), In-Vitro Library
Tutorial 5: NGS Pipeline with Automated Top Lead Selection (PacBio), Patient Library
Tutorial 6: NGS UMIs Extract and Annotation Floe
Video Tutorials Featuring AbXtract
How to Guides
How to Use the Floe Report and NGS Select to Select Population of Interest
How to Use the Floe Report and SANGER Select to Pick Population of Interest
How to Condense a Dataset with Too Many Records
I Performed Enrichment. How Do I Know which Population of My Given Sequence was Found?
How to Reduce the Number of Fields in the Output
How to Download the CSV of the Dataset of Records
How to Visualize Custom Experimental Metrics
How to upload data from an AIRR-compatible file
How to export any dataset to an AIRR-compatible file
Frequently Asked Questions
Frequently Asked Questions about AbXtract Floes
Abxtract Floes - Documentation
AbXtract/AIRR File to Orion Dataset - AbXtract
Archive To Files
Automated Top Lead Selection - AbXtract
Cluster (AbScan) Antibody Binding Regions - AbXtract
Condense Dataset by Region of Interest by Most Abundant - AbXtract
Convert floe report to html files
Custom NGS Select by Seq ID of Additional NGS Representatives by Group - AbXtract
Custom SANGER Select of Additional NGS Representatives by Group - AbXtract
Export AIRR Fields for Dataset - AbXtract
Liability Quantification Across CDRs - AbXtract
Logomaker for Antibody CDRs - AbXtract
Modify Sample Name/Barcode Group for Downstream Processing - AbXtract
Multiple Round Relative Abundance and Enrichment Calculation by Region of Interest (ROI) - AbXtract
NGS IgMatcher, Annotation Only - AbXtract
NGS Pipeline - AbXtract
NGS Pipeline Efficiency - AbXtract
NGS Pipeline with Automated Top Lead Selection - AbXtract
NGS UMIs Extract and Annotation - AbXtract
NGS and Sanger Pipeline - AbXtract
NGS and Sanger Pipeline with Automated Top Lead Selection - AbXtract
Overlap Among Different Datasets - AbXtract
Quick Sanger from ABI Traces - AbXtract
Quick Sanger from DNA or Amino Acid Sequence Files - AbXtract
Single Round Relative Abundance and Enrichment Calculation by Region of Interest (ROI) - AbXtract
Subset the Number of Fields for Export - AbXtract
Key Fields
Liability Metric Fields
Biophysical Metric Fields
Identifier Fields
Overlap Fields of NGS to SANGER or NGS
Enrichment, Abundance and Relative Abundance Fields
Scaffold / Germline Call Fields
Clustering Fields
Annotation Fields
Sequence Quality Fields
Special Fields to Add to Upload (Use in Analyze Tool Only)
AIRR Fields
Release Notes
v0.1.9 July 2024
v0.1.6 April 2024
v0.1.5 October 2023
v0.1.4 December 2022
v0.1.3 June 2022
v0.1.2 April 2022
v0.1.1 March 2022
v0.1.0 December 2021
AI Fold Floes
AI Fold Floes - Documentation
Protein Sequence to AI Folded Structure Prediction
Release Notes
v0.1.1 April 2024
v0.1.0 February 2024
Format Conversion
Orion ETL Floes - Documentation
Archive Import
Dataset Copy
Dataset to Collection Export
Dataset to File Export
Dataset to Record File Export
File to Dataset Import
Record Collection to Dataset Import
Record File to Dataset Import
URL to File Import
Format Conversion (ETL) Floes
v6.6.0 August 2025
Legacy Release Notes
v6.3.2 January 2025
v6.3.1 September 2024
v6.3.0 August 2024
v6.2.0 June 2024
v6.1.2 February 2024
v6.0.0 September 2023
v2.3.0 July 2023
v2.1.3 February 2023
v2.1.2 November 2022
v2.1.1 September 2022
v2.1.0 July 2022
v2.0.2 February 2022
v2.0.1 December 2021
v2.0.0 November 2021
v1.2.9 November 2021
v1.2.8 October 2021
v1.2.7 October 2021
v1.2.6 June 2021
v1.2.5 June 2021
v1.2.4 November 2020
v1.2.3 August 2020
v1.2.2 April 2020
v1.2.1 March 2020
v1.2.0 February 2020
v1.1.1 October 2019
v1.1.0 August 2019
v1.0.0 July 2019
v0.1.29 April 2019
v0.1.28 February 2019
v0.1.27 February 2019
v0.1.26 February 2019
v0.1.25 January 2019
v0.1.24 December 2018
v0.1.23 November 2018
v0.1.22 November 2018
v0.1.21 October 2018
v0.1.20 October 2018
v0.1.19 October 2018
v0.1.18 September 2018
v0.1.17 September 2018
v0.1.16 September 2018
v0.1.15 September 2018
v0.1.14 September 2018
Utility Floes
Introduction
Tutorials
Spruce Prep Tutorial
Creating and Applying Molecule Filters
How To Guides
How to Guides for Spruce Floes
Utility Floes - Documentation
Build Sidechains
Calculate Dipole Moment
Cap Chain Breaks
DU to Mol
DU to PDB
Dataset Append – Generating SMILES Field
Dataset Deduplication – Based on Molecule, String, Integer, or Float Field
Dataset Deduplication – Merge
Dataset Filtering – Create Custom Filter
Dataset Filtering – Custom or Built-in Filter Types
Dataset Manipulation – Add Molecule Title Field
Dataset Manipulation – Add Title to Molecule Field
Dataset Manipulation – Concatenation
Dataset Manipulation – Field Rename
Dataset Manipulation – Field Type Conversion
Dataset Subsetting – Random Splitting Or Selection
Dataset Subsetting Based on Dataset, Numerical, String, or Regex Field
Dataset Subsetting Based on String Keys
Extract Biological Units
Generate 2D Similarity Matrix
Generate 3D Similarity Matrix
Generate Fingerprints
Generate User-Defined Fingerprints
Generate and Deduplicate SMILES for One or More Datasets
Minimize Design Unit
Mutate Residue(s)
OMEGA - 3D Conformer Ensemble Generation
OMEGA - Generate a Single 3D Conformer
Protein Loop Modeling or Re-modeling
Protonate DU and structures
QUACPAC - Partial Charges
ROCS, FastROCS - Import Shape Query to Record
Receptor In DU
Residue State Changer
Rotamers of a Residue
SPRUCE - Import Prepared PDB Files
SPRUCE - Protein Preparation
Subset Design Unit
Subset Design Unit Within
Subset Design Unit to Smallest Binding Unit
Substructure Search - Small Scale Substructure Matching
Superpose DUs
Swap Metal(s)
Update DU Content
Utility Floes
v2.1.1 August 2025
Utility Floes Release Notes
v2.0.1 February 2025
Historical Release Notes
Biomolecular Modeling Floes Historical Release Notes
Cheminformatics Floes Historical Release Notes
Classic Floes Historical Release Notes
Partner Modules
The Gaussian Module
Gaussian Documentation
Gaussian Floe Tutorials
Frequently Asked Questions
OpenEye Gaussian QM Floes - Documentation
Gaussian Orion Module Release Notes
Legacy Release Notes
Format Conversion
Orion ETL Floes - Documentation
Format Conversion (ETL) Floes
Legacy Release Notes
CCDC GOLD Module
Cube Libraries
Molecular Dynamics Core Package
Installation
orionmdcore.cubes - Cube Documentation
Flask Preparation
Force Field
IO
MD Simulations
Simulation Flask Preparation
Utility
MD DataRecord
MD DataRecord a brief overview
MDDataRecord API Documentation
Molecular Dynamics Core Package Release Notes
v2.5.4 August 2025
Legacy Release Notes
v2.5.3 March 2025
v2.5.2 March 2025
v2.5.1 February 2025
v2.4.1 June 2024
v2.4.0 April 2024
v2.3.1 February 2024
v2.1.2 September 2023
v2.1.1 September 2023
v2.1.0 July 2023
v2.0.1 April 2023
v1.1.6 June 2022
v1.1.5 April 2022
v1.1.2 December 2021
Snowball - The Primary OpenEye Cube Library
Definitions of Floe Classifications
snowball - Cube Documentation
2D Depiction
2D Similarity
3D Similarity
Cheminformatics
Conformations
Debugging
Examples
Floe Report
IO
Lead Optimization
Library Design
Ligand Modeling
Ligand Preparation
Logic
MMDS
Models
Protein Ligand
SiteHopper
Spruce
Structure Based Design
Surface
Unclassified
Utility
Snowball
v0.30.1 August 2025
Legacy Release Notes
v0.29.1 February 2025
v0.28.0 July 2024
v0.27.0 February 2024
v0.26.1 September 2023
v0.26.0 July 2023
v0.25.3 December 2022
v0.24.1 September 2022
v0.24.0 July 2022
v0.23.1 December 2021
v0.20.1 June 2021
v0.20.1 November 2020
v0.19.3 August 2020
v0.19.1 August 2020
v0.18.2 April 2020
v0.17.2 November 2019
v0.16.6 September 2019
v0.16.0 July 2019
v0.15.0 June 2019
v0.14.0 June 2019
v0.13.6 March 2019
v0.13.4 November 2018
v0.13.3 September 2018
v0.13.0 August 2018
OpenEye Glossary of Terms
Legal Notices
Copyright and Trademarks
Sample Code
Citation
Orion
®
Orion Floes
Toolkits and Applications
Publications for Bibliographies
Orion
AFITT and FLYNN Applications
OEDocking Application and Toolkit
OMEGA Application and Toolkit
ROCS Application
OpenEye MMDS Web Service
Technology Licensing
GCC
GCC RUNTIME LIBRARY EXCEPTION
GNU GENERAL PUBLIC LICENSE
Orion Workflows
All OpenEye Documentation
»
Contents
»
Cube Libraries
»
Molecular Dynamics Core Package Documentation
»
Molecular Dynamics Core Package Release Notes
Molecular Dynamics Core Package Release Notes
v2.5.4 August 2025
General Notice
Relaxed OpenEye Snowball version constraint to allow versions >= 0.26.0 (upper bound removed).