2025.3
  • Release Highlights 2025.3
    • Small Molecule Discovery Suite Highlights
      • Structural Biology Floes
      • ML Model Building Floes
        • ML Build: Graph Convolution Model on Pregenerated Features for Small Molecules
  • Release Notes, Version 2025.3.1
    • Cryptic Pocket Detection Floes
      • v0.3.2 September 2025
        • General Notice
        • Minor Changes
    • Format Conversion (ETL) Floes
      • v6.7.0 September 2025
        • General Notice
        • Functional Changes
    • Machine Learning Model Building Floes
      • v1.0.2 September 2025
        • Feature Updates
        • New Floes
    • Molecular Dynamics Affinity
      • v 6.5.7 September 2025
        • General Notice
    • Molecular Dynamics Core Package
      • v2.5.5 September 2025
        • General Notice
        • Updates
        • Bug Fixes
    • pKa Prediction Floes
      • v0.2.0 September 2025
        • General Notice
        • Feature Updates
    • Structural Biology Floes
      • v0.1.2 September 2025
        • General Notice
  • 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
      • Structural Biology Floes
        • Introduction
        • Tutorials
        • OpenEye Structural Biology Floes - Documentation
        • Structural Biology Floes
        • Bibliography
      • Utility Floes
        • Introduction
        • Tutorials
        • How To Guides
        • Utility Floes - Documentation
        • Utility Floes Release Notes
        • Utility Floes Legacy 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
        • OpenEye pKa Prediction Floes - Documentation
        • pKa Prediction Floes
        • 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 Release Notes
        • Utility Floes Legacy 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
        • 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
        • Legacy Release Notes
      • Permeability Floes
        • Tutorials
        • OpenEye Permeability Floes - Documentation
        • Release Notes
      • pKa Prediction Floes
        • Introduction
        • Tutorials
        • Frequently Asked Questions
        • OpenEye pKa Prediction Floes - Documentation
        • pKa Prediction Floes
        • 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 Release Notes
        • Utility Floes Legacy 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 Sequences to 3D Models
        • Antibody SiteHopper-based Clustering
        • Antibody Structure Relaxation
        • Antibody Subset System
        • Antibody Surface Patch Generation
        • Import Antibody FASTA Files
        • Renumber and Restyle Antibody
      • Release Notes
        • v0.1.11 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
        • File(s) and/or dataset(s) to archive
        • Record Collection to Dataset Import
        • Record File to Dataset Import
        • URL to File Import
      • Format Conversion (ETL) Floes
        • v6.7.0 September 2025
      • Legacy Release Notes
        • v6.6.0 August 2025
        • 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 Release Notes
        • v2.1.2 September 2025
      • Utility Floes Legacy Release Notes
        • v2.1.1 August 2025
        • 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
      • MD DataRecord
        • MD DataRecord a brief overview
        • MDDataRecord API Documentation
      • Molecular Dynamics Core Package
        • v2.5.5 September 2025
      • Legacy Release Notes
        • v2.5.4 July 2025
        • v2.5.3.1 September 2025
        • 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
        • v0.30.2 Sept 2025
      • Legacy Release Notes
        • v0.30.1 August 2025
        • 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
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  • Structural Biology Floes »
  • OpenEye Structural Biology Floes - Documentation

OpenEye Structural Biology Floes - Documentation

  • Automated WEMD Simulation and Best Structure Search Guided By Eigen CryoEM Maps
  • Automated WEMD Simulation and Best Structure Search Guided by Target CryoEM Map
  • Continue WEMD Simulation Guided by CryoEM Maps
  • Cryo-EM Map Best Structure Search from WEMD Simulation
  • Generate Most Probable Path from WEMD Simulation
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