Release 2024.2
Release Highlights
Updated Floes
Small Molecule Packages
Biomolecular Modeling
Cheminformatics
Classic Floes - OpenEye Applications in Orion
Cryptic Pocket Detection
Format Conversion
Generative Chemistry
Large Scale Floes
Machine Learning Model Building Floes
Molecular Dynamics Affinity Package
Molecular Dynamics Core Package
Permeability Floes
Quantum Mechanics Psi4 Floes
Snowball - The Primary OpenEye Cube Library
The Gaussian Module
Gaussian Documentation
Antibody Packages
AbXtract™ - NGS Antibody Discovery
3D Antibody Modeling Package
3D QSAR Models
Introduction
Theory
A Model of Multiple Models
Model Descriptors
Machine Learning Methods
Gaussian Process Regression (GPR)
Kernel Partial Least Squares (kPLS)
3D Conformer Generation
Stereoisomer Handling
Applicability Domain and Prediction Confidence
Model Interpretation
Tutorials
Datasets
3D QSAR Model: Builder Floe
Running the Floe with Provided Pre-aligned Conformers
Running the Floe Using
Posit
as Conformer Generation and Alignment Method
3D QSAR Model: Predictor Floe
3D QSAR Model: Validation Floe
3D QSAR Model: Interpretation Floe
OpenEye 3D QSAR Models - Floe Documentation
3D QSAR Model: Builder
3D QSAR Model: Interpretation
3D QSAR Model: Predictor
3D QSAR Model: Validation
OpenEye 3D QSAR Models - Cube Documentation
Descriptor Calculation
Descriptors Calculated for Bulk Storage
Model Descriptors
PLIF IntHint
Hyperparameter Optimization
Model Optimization: ROCS and Kernel-PLS Regression
Ligand Preparation
Pose Generation with Flexible Overlay
Pose Generation with Hybrid
OMEGA
Model Building
Model Builder: 3D Regression (Features Parameter)
Model Builder: 3D Regression (Features Port)
Model Validation: Average
Model Interpretation
Generate Probe Atoms
Generate Probe Surfaces
Model Prediction
Model Consensus Validation: 3D
Model Cross Validation
Model Predictor: 3D Regression
Model Predictor: Kernel-PLS Regression
Report Generation
Cross Validation Statistics Report
External Validation Statistics Report
Generate KPLS Optimization report
Model Report
Statistics
Calculate Validation Statistics
Utility
Add Ref Title
Add Tag to Record
Auto Choose Pose Generation Method
Check Potency Data
Check if Stereo Specified
Distribute KPLS Optimization
Filter Records by Posit Probability
Find Query Molecule
Generate Index
KPLS Optimum Number of Features Merge
Load External Descriptors
Merge KPLS Optimization Records
Merge Records to a Vector
Model Reader: Molecules Information
Model Reader: Receptor Information
Model Selector
Pick Best Stereo Conformer
Pick Optimal Feature for KPLS
Pick Pose Generation Method
Pick Pose Generation Method (Port Input)
Probe Generation Distributor
Probe Generation Switch
Receptor Selection for Pose Mode Auto
Remove DU
Sort Records by Index
Split Records for Training and Test
Split Records from Vector
Benchmark Results
Comparison to 3rd-party Software
BACE-1
Sutherland Datasets
Release Notes
v1.0.0 February 2024
General Notice
New Floes
Bibliography
AI Fold Floes
AI Fold Floes - Documentation
Protein Sequence to AI Folded Structure Prediction
Release Notes
v0.1.1 April 2024
General Notice
Floe Updates
v0.1.0 February 2024
General Notice
Biomolecular Modeling
Tutorials
Search for Similar Binding Sites with SiteHopper
Create a Tutorial Project
Prepare Patch Dataset
Prepare Query Protein
Search Patch Dataset
Biomodeling Floes - Documentation
Build Sidechains
Cap Chain Breaks
DU to Mol
DU to PDB
Enumerate Pockets on Design Units
Extract Biological Units
Make SiteHopper Patch Database
Make SiteHopper Patch Database in SHDB format
Minimize Design Unit
Mutate Residue(s)
Protein Loop Modeling or Re-modeling
Protonate DU and structures
Residue State Changer
Rotamers of a Residue
SiteHopper Search
Subset Design Unit
Subset Design Unit Within
Subset Design Unit to Smallest Binding Unit
Superpose DUs
Swap Metal(s)
Update DU Content
Release Notes
v0.4.1 July 2024
General Notice
Floe Updates
v0.3.9 February 2024
General Notice
Floe Updates
v0.3.8 July 2023
General Notice
Floe Updates
v0.3.6 December 2022
General Notice
Floe Updates
v0.3.5 September 2022
General Notice
Floe Updates
v0.3.2 July 2022
General Notice
Floe Updates
v0.3.1 December 2021
General Notice
Floe Updates
Data Updates
Documentation Updates
v0.2.1 June 2021
General Notice
Floe Updates
Documentation Updates
v0.2.0 November 2020
General Notice
Documentation Updates
Floe Updates
v0.1.1 August 2020
General Notice
Floe Updates
v0.1.0 April 2020
General Notice
CCDC GOLD Floes
Cheminformatics
Tutorials
Deciding on Clustering Method
Floes used in this Tutorial
Decision Tree
Size Constraints
Application-Based Clustering
Small Scale Clustering
Clustering Methods Overview
DBSCAN Clustering
K-Medoids Clustering
Hierarchical Clustering
Large Scale Clustering
Hitlist Clustering
Diverse Subset Floes
Large Scale Clustering
Diverse Subset
Floes used in this Tutorial
Required Inputs
Outputs
Troubleshooting
Creating and Applying Molecule Filters
Floes used in this Tutorial
Create a Custom Filter
Filter Customization
Parameter Settings
Functional Group Parameters
Create Custom Filter Floe Output
Run a Custom Filter
Troubleshooting
Hitlist Clustering
Floes used in this Tutorial
Required Inputs
Floe Report
Troubleshooting
Large Scale Clustering
Floes used in this Tutorial
Input Size
Algorithm: Directed Sphere Exclusion
Step 1: Generate N new cluster heads
Step 2: Assign cluster members to existing cluster heads
Sphere Exclusion Radius
Troubleshooting
Floe Runtime is Too High
Floe Cost is Too High
Memory Limit Exceeded
Advanced Parameter Descriptions
References
cheminfo - Documentation
2D Diverse Subset
2D Hitlist Clustering
3D Diverse Subset
3D Hitlist Clustering
Calculate Average Precision
Count Molecules in Fast Substructure Search Collection
DBSCAN 2D Similarity Clustering
DBSCAN 3D Similarity Clustering
Dataset Append – Generating SMILES Field
Dataset Classification – Bemis-Murcko
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
Fast Fingerprint Similarity Search
Fast Substructure Search with SMARTS
Fast Substructure Search with an MDL Query
Generate 2D Similarity Matrix
Generate 3D Similarity Matrix
Generate Fingerprints
Generate User-Defined Fingerprints
Generate and Deduplicate SMILES for One or More Datasets
Hierarchical 2D Similarity Clustering
Hierarchical 3D Similarity Clustering
K-Medoids 2D Similarity Clustering
K-Medoids 3D Similarity Clustering
Large Scale 2D Similarity Clustering
Large Scale 3D Similarity Clustering
MultistatePKaModel Based Ionization States Enumeration Floe
Prepare Collection for Fast Similarity or Substructure Search from Dataset
Prepare Collection for Fast Similarity or Substructure Search from File
Release Notes
v1.3.1 July 2024
General Notice
Floe Updates
v1.3.0 January 2024
General Notice
Floe Updates
v1.2.0 July 2023
General Notice
New Floes
Floe Updates
v1.1.0 December 2022
General Notice
New Floes
Floe Updates
v1.0.0 July 2022
General Notice
New Floes
Floe Updates
v0.2.4 December 2021
General Notice
New Floes
Floe Updates
v0.2.3 June 2021
General Notice
New Floes
Floe Updates
v0.2.2 December 2020
General Notice
v0.2.1 November 2020
General Notice
v0.2.0 August 2020
General Notice
v0.1.1 April 2020
General Notice
New Floes
Classic Floes - OpenEye Applications in Orion
Tutorials
BROOD Floe Tutorial
Floes Used in the Tutorials
Input Parameters
BROOD Query Preparation
Running in ET and linkOnly modes
Interpretation of Results
CHOMP Floe Tutorial
Floes Used in the Tutorials
Input and Output Parameters
Fragment Filtering Parameters
Guidelines for Control Parameters
Interpretation of Results
Spruce Prep Tutorial
Floes Used in the Tutorials
Run the Protein Preparation Floes
Run the Protein Preparation Floes Using a Reference Design Unit
Reviewing the Floe Reports
Analyzing the Results
Next Steps
Gameplan Tutorial
Floes used in the Tutorials
Prepare Protein and Bound Ligand from PDB Codes
Run the Gameplan Floe
Gameplan Results
Next Steps
Filtering Docking Hits by Interactions Tutorial
Floes used in the Tutorial
Run the Floe
Exploring the Interaction Fingerprints
Filtering the Docked Poses
Next steps
How To Guides
How to Guides for Spruce Floes
How can I provide Spruce information about the bound ligand?
How can I generate a prepared design unit for an un-liganded structure?
How do I edit a prepared design unit?
Frequently Asked Questions
Frequently Asked Questions for Spruce Floes
What input formats does Spruce accept, and what are the requirements?
What is a reference design unit (DU) used for, and when should I provide one?
Spruce generated multiple design units from a structure, which one should I pick?
OpenEye Classic Floes - Documentation
BROOD - 3D Fragment Replacement
BROOD - 3D Fragment Similarity
BROOD - DB File to Collection
BROOD - Fragments Conformer Generation
BROOD - Query Builder
CHOMP - Generate BROOD Fragment Database
Calculate Atropisomerism
Calculate Dipole Moment
EON - Shape and Electrostatic Similarity Alignment
Filter Docking Hits by Interactions
Fingerprint Search - Small Scale 2D Similarity
FreeForm - Aqueous Ligand Configurational Free Energies with SZYBKI
FreeForm - Bound Ligand Configurational Free Energies with SZYBKI
FreeForm - Ligand Solvation Energies with SZYBKI
GamePlan - Ligand Design with Water Analysis using SZMAP
OEDocking - Dock into an Active Site for Virtual Screening
OMEGA - 3D Conformer Ensemble Generation
OMEGA - Conformer Generation for Macrocycles
OMEGA - Generate a Single 3D Conformer
POSIT - Ligand Guided Small Molecule Posing
QUACPAC - Partial Charges
QUACPAC - Tautomer Enumeration and Analysis
ROCS - Shape Based Alignment for Virtual Screening
ROCS Query Model Builder
ROCS, FastROCS - Import Shape Query to Record
Receptor In DU
SPRUCE - Import Prepared PDB Files
SPRUCE - OEDesignUnit Format Type Updater
SPRUCE - Protein Preparation
SZYBKI - Ligand Minimization in a Flexible Active Site
SZYBKI - Ligand Minimization in a Rigid Active Site
SZYBKI - Single point MMPBSA
SZYBKI - Small Molecule Hydrogen-Only Minimization
SZYBKI - Small Molecule Minimization
Substructure Search - Small Scale Substructure Matching
Release Notes
v0.14.0 July 2024
General Notice
Floe Updates
v0.13.1 February 2024
General Notice
Floe Updates
v0.12.1 September 2023
General Notice
v0.12.0 July 2023
General Notice
Floe Updates
v0.11.2 December 2022
General Notice
Floe Updates
v0.10.1 September 2022
General Notice
Floe Updates
v0.10.0 July 2022
General Notice
New Floes
Floe Updates
v0.9.0 December 2021
General Notice
New Floes
Floe Updates
v0.8.3 June 2021
General Notice
New Floes
Floe Updates
v0.7.1 November 2020
General Notice
Floe Updates
v0.6.2 August 2020
General Notice
v0.6.1 August 2020
General Notice
New Floes
Floe Updates
Removed Floes
v0.5.2 April 2020
General Notice
New Floes
Floe Updates
v0.4.0 November 2019
General Notice
New Floes
Floe Updates
v0.3.6 September 2019
General Notice
New Floes
Floe Updates
v0.3.3 July 2019
General Notice
v0.3.1 June 2019
General Notice
New Floes
Floe Updates
v0.2.5 March 2019
General Notice
New Floes
Floe Updates
v0.2.2 September 2018
General Notice
Floe Updates
Cryptic Pocket Detection
Introduction
Tutorials
Preparing Input
Design Unit Preparation Using a MMDS Reference Structure (Option 1)
Design Unit Preparation Without a MMDS Reference Structure (Option 2)
Subset the Design Unit
Basic Tutorial: Automated Cryptic Pocket Detection with Probe Occupancy Analysis
Search and Run the Floe in Orion
Visualize Cryptic Pocket Analysis Report and Pocket Receptors
Failure Report
Advanced Tutorials
Solvate and Equilibrate Target Protein
Calculate Normal Modes
Run a Weighted Ensemble MD Simulation
Perform Weighted Ensemble MD Analysis
Dynamic Probe Analysis
Exposon Analysis
Probe Occupancy Analysis
Frequently asked questions
How should the starting structure be selected for running the cryptic pocket detection floes?
Automated cryptic pocket detection floe fails due to a memory error. How to troubleshoot the job failure?
OpenEye Cryptic Pocket Detection Floes - Documentation
Automated Cryptic Pocket Detection with Probe Occupancy Analysis
Calculate Normal Modes
Continue a Weighted Ensemble MD Simulation
Dynamic Probe Binding Analysis
Exposon Analysis
Perform Weighted Ensemble MD Analysis
Probe Occupancy Analysis
Run a Weighted Ensemble MD Simulation
Solvate and Equilibrate Target Protein
Release Notes
v0.2.4 July 2024
General Notice
Minor Changes
v0.2.2 April 2024
General Notice
Major Changes
Minor Changes
v0.1.2 September 2023
General Notice
Minor Changes
v0.1.0 July 2023
General Notice
Bibliography
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
Release Notes
v6.2.0 July 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
Bugfixes
v0.1.27 February 2019
v0.1.26 February 2019
Bugfixes
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
Generative Chemistry
Generative Structure Floes - Documentation
Focused Library - Core Input
Focused Library - Molecule Input
General Considerations
Focused Library - Reagent Join
Focused Library - Synthon Analogs
General Considerations
Generative Structure Floe
Generative Structure Floe - Site selection
Generative Structure Indexing - Graft Database Generator
Generative Structure Indexing - MMP Molecule Indexer
Generative Structure Indexing - MMP Transform Extractor
Reaction & Reagent Database - Create from BULK SMILES
Launching the Floe
Reaction & Reagent Database - Create from Dataset
Launching the Floe
Reaction & Reagent Database - Create from ZINC Download
ZINC Subset Selection
Launching the Floe
Reaction & Reagent Database - Directory Listing
Reaction & Reagent Database - Half Reaction Generator
Reaction & Reagent Database - Launch Product Enumerations
Reaction & Reagent Database - Product Enumeration Summary
Reaction & Reagent Database - Reaction Definition Validator
Reaction & Reagent Database - Reagent Definition Generator
Reaction & Reagent Database - Reagent Molecule Classification
Reaction & Reagent Database - Retrieve Reaction Reagents
Release Notes
v0.9.3 July 2024
Updates to the Generative Design Floes - Base & Advanced Packages
v0.7.1 September 2023
Updates to the Generative Design Floes - Base & Advanced Packages
v0.7.0 July 2023
Updates to the Generative Design Floes - Advanced Package
Bug fixes and features
v0.6.0 December 2022
Bug fixes and features
v0.5.1 September 2022
Bug fixes and features
v0.5.0 July 2022
Enhancements to reaction definitions
General enhancements
Updates to the Generative Design Floes package
Updates to the Generative Design Floes - Advanced package
Updates to the Generative Design Floes - MaaS package
v0.4.0 December 2021
Enhancements to reaction definitions
Additional enhancements
Updates to the Generative Design Floes package
Updates to the Reaction Floes - Advanced package
v0.3.2 July 2021
v0.3.1 June 2021
v0.2.14 November 2020
v0.2.13 November 2020
v0.2.12 August 2020
v0.2.11 May 2020
Large Scale Floes
Tutorials
Dock Ten Million Molecules with Gigadock Warp and Analysis with Freeform Consensus
Create a Tutorial Project and Working Directory
Prepare Design Unit / Receptor
View Prepared Design Unit / Receptor
Dock Molecules to Site
Compute Freeform Delta G of the Hit List Molecules
Compute Consensus of Docking Score and Freeform Delta G
View Results
Dock One Million Molecules with Gigadock Floe
Create a Tutorial Project and Working Directory
Prepare Design Unit / Receptor
View Prepared Design Unit / Receptor
Prepare One Million Input Molecules
Dock Molecules to Site
Cluster Hit List Poses from Gigadock
View Results
FastROCS Plus with Freeform Analysis
Create a Tutorial Project and Working Directory
Create a Dataset with Revlimid
Run the FastROCS Plus Floe
Compute Freeform Delta G of the Hit List Molecules
View hit list results
FastROCS Plus with Docking and Consensus Score of Top Molecules
Create a Tutorial Project and Working Directory
Prepare Design Unit / Receptor
View Prepared Design Unit / Receptor
Run the FastROCS Plus Floe
View Consensus Result
Prepare Vendor Database for Giga Docking and FastROCS
Create a Tutorial Project and Working Directory
Import Mcule Database into Orion
Create GigaDocking and FastROCS collections
View Collection Properties
View of Random Sample of the Collection
How-to Guides
Run Giga Docking on Billions of Molecules
Context
Procedure
Estimate the cost of a Giga Docking Run
Context
Procedure
Determine if Giga Docking Will Give Good Results with a Given Receptor
Context
Procedure
Edit a Receptor
Context
Procedure
Generate a Giga Docking Hit List Datast of More Than 10K Molecule
Context
Procedure
Prepare Molecules in a CSV File for GigaDocking and FastROCS
Context
Procedure 1 : Identify the title column
Procedure 2 : Prepare the molecules without titles
Restart a Giga Docking Job That Stopped Due to Cost
Context
Procedure
Get Access To Full Vendor Giga Docking Collections Prepared by OpenEye
Context
Procedure
Floe Reference Material
Gigadock
Description
Details
Parameters
FastROCS Plus
Description
Details
Parameters
Batch FastROCS
Description
Details
Parameters
Prepare Giga Collections
Description
Details
Parameters
Filter Collection
Description
Details
Parameters
Collection to Hitlist Dataset
Description
Details
Parameters
FreeForm Pose
Description
Details
Parameters
Cluster Poses
Description
Details
Parameters
Collection Info
Description
Details
Parameters
Sample Collection
Description
Details
Parameters
Collection to File
Description
Details
Parameters
Gigadock Collection to Hi-res FastROCS Collection
Description
Details
Parameters
Pareto Frontier Consensus
Description
Details
Parameters
Gigadock Warp
Description
Details
Parameters
Multi Query 2D Similarity
Description
Details
Parameters
Explanations
Gigadock Warp Details
Overview
Method
Performance Compared to
floe_#01_large_scale_docking_floe
Datasets vs. Files. vs. Collections
Datasets
Files
Collections
Control the Cost of a Giga Docking Run
Context
Receptor / Design Unit
Docking Mode
Docking Molecules
Giga Docking Cost Threshold
FastFred
Pareto Frontier Explanation
Release Notes
4.1.9 July 2024
Highlights
Bug Fixes
4.1.5 February 2024
Highlights
Features
Changes
Bugfixes
4.0.2 September 2023 (Large Scale Floes Hotfix)
Changes
Bugfixes
4.0.0 July 2023 (Orion Floe 2023.1 Release)
Highlights
Changes
Bugfixes
3.4.5 December 2022 (Orion 2022.4 Release)
New Features
Bugfixes
3.3.4 September 2022
Bugfixes
3.3.0 June 2022 (Orion 2022.2 release)
Features
Changes
Bugfixes
3.2.0 April 2022 (Orion 2022.1 release)
Changes
Minor Features
Bugfixes
3.1.7 Dec 2021 (Orion 2021.2.1 release)
Highlights
General Notice
New Features
Changes
Fixes
3.0.3 Oct 2021 (hotfix)
Fixes
3.0.2 Jun 2021 (Orion 2021.1 release)
General Notice
New Features
Fixes
2.0.6 April 2021 (hotfix)
Fixes
2.0.0 Nov 2020 (Orion 2020.3 release)
General Notice
New Features
Fixes
0.1.0 August 2020 (Orion 2020.2 release)
General Notice
New Features
Fixes
Machine Learning Model Building Floes
Introduction
Introduction
Tutorials
Layout of the Machine Learning Model Building Package
Data Preprocessing Floe
Machine Learning Model Building
Molecular Property Prediction using Built Models
Setup Directions for the Machine Learning Model Building Tutorials
Create a Tutorial Project
Floe Input
Run the ML Model Building Floes
Data Processing of Small Molecules for ML Model Building Floes
Floe Input
Run the Generic Property Prediction Floe
Analyze the Output
Analyze the OEModel Floe Report
Scaffold Split
Tutorials to Build Machine Learning Models
ML Build: Regression Model with Tuner using Fingerprints for Small Molecules
Floe Input
Run the Model Building Floe
Analysis of Output and Floe Report
ML Build: Cheaper and Faster Machine Learning Regression Models with Tuner using Fingerprints for Small Molecules
Floe Input
Run OEModel-Building Floe
Analysis of Output and Floe Report
ML Build: Classification Model with Tuner using Fingerprints for Small Molecules
Floe Input
Run OEModel Building Floe
Analysis of Output and Floe Report
ML Build: Regression Model with Tuner on User-Based Feature Vector Input
Floe Input
Run OEModel Building Floe
Analysis of Output and Floe Report
ML ReBuild: Transfer Learn ML Regression Model Using Fingerprints for Small Molecules
Floe Input
Run OEModel Building Floe
Analysis of Output and Floe Report
Tutorials to Predict Molecules based on trained Machine Learning Models
ML Predict: Use Pretrained Regression Models to Predict Properties of Molecules
Floe Input
Run Generic Property Prediction Floe
Analyze OEModel Floe Report
Analyze Output
ML Predict: Use Pretrained Classification Fingerprint Model to Predict Properties of Molecules
Floe Input
Run Classification Property Prediction Floe
Analyze OEModel Floe Report
Analyze Output
ML Predict: Regression using Feature Input Floe
Floe Input
Run a Generic Property Prediction Floe
Analyze OEModel Floe Report
Analyze Output
Predict the Solubility of Small Molecules
Floe Input
Run OEModel-Apply Floe
Analyze OEModel Floe Report
Analyze Output
Predict hERG Toxicity of Drug-Like Molecules
Floe Input
Run hERG Toxicity Floe
Analyze OEModel Floe Report
Analyze the Output
How-To Guides
How to Build an
Optimal
Property-Predicting Machine Learning Model by Tweaking Neural Network Architecture
Fully Connected Feed-Forward Neural Network (
F
nn
)
How to Use LIME Explainer to Understand and Analyze Machine Learning Predictions
Library Details of the Floe
How to Use Built Machine Learning Models for Property Prediction and Verification of Unseen Molecules
Library Details of the Floe
Floe Reference Documentation
Data Processing of Small Molecules for ML Model Building
ML Build: Regression Model with Tuner using Fingerprints for Small Molecules
ML Build: Classification Model with Tuner using Fingerprints for Small Molecules
ML Build: Regression Model with Tuner using Feature Input
Solubility Prediction for Small Molecules using ML and Cheminfo Fingerprints
Training Data Details
ML Predict: Regression using Fingerprints for Small Molecules
ML Predict: Classification using Fingerprints for Small Molecules
ML Predict: Regression using Feature Input
ML ReBuild: Transfer Learn ML Regression Model using Fingerprints for Small Molecules
hERG Toxicity Prediction for Small Molecules using ML and Cheminfo Fingerprints
Training Data Details
Theory
Theory: The Application of Neural Networks to OpenEye Model Building
Fully Connected Feed Forward Neural Network (
F
nn
)
Explaining Predictions Using LIME
FAQs
Frequently Asked Questions
For the model building floes, how do you compare multiple models to decide which one is the best?
How good is your solubility model?
Does the model use or train on 3D features?
The inputs are still based on expert parameters such as fingerprints, which are all biased by the rules defined by the expert user. Any insights into how to overcome this flaw?
Are the predictions for crystalline solubility? Is the data for crystals?
What data was used to train hERG toxicity Model?
Why do you prefer neural networks instead of something like XGBoost?
Neural networks don’t always show good performance in low data regimes. What measures do you take to improve performance?
How are the confidences computed?
What methods do you find most effective to eliminate overfitting of your models?
What percentages do the solubility predictions have for high or medium confidences?
In the model builder floes, am I restricted to fingerprints, or can I add other descriptors, such as molecular properties or other calculated or experimental parameters?
Bibliography
Reference and Bibliography
Release Notes
Release Notes
v0.12.0 July 2024
v0.11.1 July 2023
v0.10.5 March 2023
v0.10.0 December 2022
v0.9.2 September 2022
v0.9.0 July 2022
Molecular Dynamics Affinity Package
Introduction
MD Affinity Floes
Induced-Fit Posing (Confined) Floe
How-To Guide and Tutorials
MD Affinity Floes
Short Trajectory MD with Analysis
Nonequilibrium Switching
Edge Mapper for RBFE Calculations
Plain MD
Bespoke and Custom Force Field
Structured Water Analysis
Using the Recovery Dataset for MD Floes
Induced-Fit Posing (Confined) Floe
Induced-Fit Posing (Confined)
MD Affinity Floes - Documentation
Analyze Protein-Ligand MD [MDAnalysis]
Associate Force Field Offxml Files With Ligand Record [Utility]
Bound Protein-Ligand MD [MDPrep] [MDRun]
Compare Experimental Affinity with End Point Analysis Results [Utility]
Compare Induced-Fit Posing (IFP) Results to Target Receptor [IFP]
Convert MD Analysis results to Cluster-Centric Dataset [Utility]
Edge Mapper for RBFE calculations [FECalc]
Equilibration and Nonequilibrium Switching [MDPrep] [MDRun] [FECalc]
Extract Short Trajectory MD Results for Download [Utility]
Induced-Fit Posing (Confined) [IFP]
Induced-Fit Posing (IFP) Prep: Pruning reference receptor for docking [IFP]
Ligand Bound and Unbound Equilibration for NES [MDPrep] [MDRun]
MD API Dataset Converter [Utility]
NES Result Utilities [Utility] [FECalc]
Nonequilibrium Switching Recovery [Utility] [FECalc]
Nonequilibrium Switching [MDRun] [FECalc]
Plain Gromacs [MDRun]
Plain Molecular Dynamics [MDRun]
Short Trajectory MD with Analysis [MDPrep] [MDRun] [MDAnalysis] [STMD]
Solvate and Run MD [MDPrep] [MDRun]
oemdaffinity.cubes - Cube Documentation
Affinity Analysis
Affinity Plot
Analysis
2-traj MMPBSA
Analyze Water Cube
Calculate Grid-Based Water Cube
Cluster Ligand Traj OEMol
Clustered Water Analysis Cube
Compute BintScore for Initial Pose and Trajectory
Concatenate Trajectory BintScor Components
Concatenate Trajectory MMPBSA Energy Components
Conf Trajs To Ligand Traj
Generate Ligand Floe Report HTML from Protein-Ligand MD Traj Analysis.
Initialize Water Analysis Cube
MD Conformer Gathering Data
MDExtractDataCube
MDFloeReportCube
MDFloeWriteClusterCentricDataset
Make Cluster Protein and Ligand average and median OEMols
NMax Waters
Population Analysis of Traj Clusters
Prepare the Traj Analysis Dataset for Reporting
STMD Result to File
STMD Result to Tarball File
Traj to OEMol Cube
Trajectory Interaction Energies
Trajectory Poisson-Boltzmann and Surface Area Energies
Trajectory Stride Setting Cube
Unbound Cluster Ligand Traj OEMol
Unbound Conf Trajs To Ligand Traj
Unbound MD Conformer Gathering Data
Unbound Population Analysis of Traj Clusters
Unbound Traj MMPBSA
Unbound Traj to OEMol Cube
Flask Preparation
Ligand Preparation For Pytest
Free Energy Calculations
BARoverlapTest
DDGAggregator
LigandClusterSelection
NESAnalysis
NESEdgeFloeReport
NESGMX
NESGMXChimera
NESResultToFile
OEMapper
OEMapperFloeReport
OEMapperResultToFile
PlotNESResults
PredictDGFromDDG
RBFECEdgeGathering
ReadChimeraMCSTests
TestChimeraMCS
IFP Analysis
Add Receptor Type Cube
Cluster Cube
Compute BintScore for Initial Pose and Trajectory (IFP)
Compute Score Cube
Compute Step1 Score Cube
Concatenate Trajectory BintScore Components (IFP)
Docking Checker Detection
Extract Clus Avg
Generate Ligand Floe Report HTML for IFP summary.
IFD Output Prep Cube
IFP Order Output Records Cube
IFP Rank Setting Cube
IFP Report Info Gather Cube
IFP Update Info Dict Cube
MDCompToDuCube
Minimized Pose Gathering Cube
POSIT Gathering Cube
Population Analysis of Traj Clusters (IFP)
Pose MMPBSA and BintScore
Reset AtomIdx Cube
IFP Input Checker
Optional Pruned Receptor Input Checker
Target Receptor Input Checker Cube
IFP MD Simulations
Minimization Cube for IFD
IFP Preparation
Active Site Detection
Active Site Pruning
Additional POSIT Switch
Set MapIdx Cube
Input Checker
Affinity File Format Checker
Bound Dataset Health Checker
PL Traj Analysis Input Checker Cube
Solvate and Run MD Input Checker Cube
MD Analysis
MD End Point Analysis Results to File
MD Simulations
Bound Protein Ligand MD Health Checker
MD Recover Restart for ProxyCube
Specify Protein Tumbling Restraints
Simulation Flask Preparation
Bound and UnBound Splitting Cube
Simulation Flask ID Setting
Structure Based Design
Posit
Unbound Simulation Preparation
FreeForm Output Ligand Setting
Unbound FreeForm
Unbound Ligand Preparation
Unclassified
SMIRNOFF Force Field Files Loader
Release Notes
v 6.4.3 July 2024
General Notice
Floe Updates
New Cubes
Cube Updates
v 6.3.6 April 2024
General Notice
Floe Updates
New Cubes
Cube Updates
v 6.2.1 February 2024
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
v 6.1.7 September 2023
General Notice
v 6.1.4 September 2023
General Notice
Floe Updates
Cube Updates
v 6.1.2 July 2023
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
v 6.0.3 April 2023
General Notice
Floe Updates
New Cubes
Cube Updates
v 5.6.1 December 2022
General Notice
Floe Updates
New Cubes
Cube Updates
v 5.5.3 September 2022
General Notice
Cube Updates
Compatibility Notice
v 5.5.0 July 2022
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
v 5.0.5 April 2022
New Floes
Floe Updates
New Cubes
Cube Updates
v 5.0.3 December 2021
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
v 4.0.1 June 2021
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
v3.0.1 November 2020
General Notice
v2.0.0 September 2020
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
v1.0.0
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
v0.9.6
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
v0.9.4
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
Molecular Dynamics Core Package
Installation
orionmdcore.cubes - Cube Documentation
Flask Preparation
Collection Setting
Complex Preparation
Ligand Charge
Ligand Setting
Receptor Components
Record Size Checking
Solvation
Force Field
Apply Force Field
MD Simulations
Delete MD Stages
Iterative NPT Cube
MD Cycle Checkpoint
MD ProxyCube
MD Recover Restart for ProxyCube
MD Speed Checker Cube
Minimization Cube
NPT Cube
NVT Cube
Simulation Flask Preparation
Bound and UnBound Switching Cube
Simulation Flask ID Setting
Utility
MD API Dataset Converter Cube
MD DataRecord
MD DataRecord a brief overview
MD DataRecord structure
Code snippets
MDDatatecord API Documentation
Release Notes
v2.4.3 July 2024
Cube Updates
Bug Fixes
v2.4.0 April 2024
Cube Updates
Bug Fixes
General Notice
v2.3.1 February 2024
API-Breaking Changes
New Features
Bug Fixes
General Notice
v2.1.2 September 2023
Bug Fixes
v2.1.1 September 2023
New Features
v2.1.0 July 2023
General Notice
Cube Updates
v2.0.1 April 2023
General Notice
New Cubes
Cube Updates
v1.1.6 June 2022
General Notice
New Cubes
Cube Updates
v1.1.5 April 2022
General Notice
New Cubes
Cube Updates
v1.1.2 December 2021
General Notice
New Cubes
Cube Updates
Permeability Floes
Tutorials
A Small Molecule Membrane Permeability Calculation
Create a Tutorial Project
Launch a Permeability Simulation Job
Analyze the Permeability Simulation
Calculate the Auxiliary Coordinates
OpenEye Permeability Floes - Documentation
Permeability - Analyze Permeability Simulation
Permeability - Calculate Auxiliary Coordinates (Optional)
Permeability - Continue Permeability Simulation (Optional)
Permeability - Run Permeability Simulation
permeability.cubes - Cube Documentation
Analysis Cubes
Auxiliary Coordinates
Permeability
Structure
Report Cubes
Permeability Auxiliary Calculation Report
Permeability Report
WESTPA Multi-Stage Rate Report
Simulation Cubes
Data Storage
System Preparation
Weighted Ensemble
Release Notes
v0.1.6 July 2024
General Notice
Floe Updates
Documentation Updates
v0.1.5 September 2023
General Notice
Floe Updates
Documentation Updates
v0.1.4 July 2023
General Notice
Floe Updates
Documentation Updates
v0.1.3 December 2022
General Notice
Floe Updates
Documentation Updates
Minor Changes
v0.1.2 September 2022
General Notice
v0.1.1 July 2022
General Notice
Floe Updates
Documentation Updates
Minor Changes
v0.1.0 April 2022
General Notice
Quantum Mechanics Psi4 Floes
Psi4 QM Floes
Psi4 HF3c Dipole Moment
Psi4 QM Complete Molecule Torsion Scan
Psi4 QM Conformer Ensemble
Psi4 QM Fragmentation and Torsion Scanning
Psi4 QM Geometry Optimization
Psi4 QM Interaction Energy
Psi4 QM Local Minima Search
Psi4 QM Property Calculation
Psi4 QM SMARTS Torsion Scan
Psi4 QM Tautomer Floe
Psi4 QM UI Atom Selection Torsion Scanning
Psi4 QM Vacuum Entropy Floe
How-To Guides
How to Generate Conformers with a Custom Torsion Library
Create an Input Dataset
Run the Fragmentation and Torsion Scanning Floe
Understanding the Torsion Scan Floe Report
Generate Conformers with Your Custom Torsion Rules
Understanding the Conformer Ensemble Floe Report
How to Run Benchmark Floes for Cost Estimation
Benchmark Torsion Scanning Floes
Benchmark Conformer Generating Floes
Benchmark Property Calculation and Geometry Optimization Floes
Frequently Asked Questions
When should I change the memory or thread count?
How do I check the metrics (memory, CPU usage) in a QM calculation?
How much will my floe cost?
What method and basis set should I use?
Why are my calculations failing due to the presence of implicit hydrogens?
Release Notes
v1.3.0 July 2024
Floe Updates
v1.2.0 July 2023
Floe Updates
v1.1.4 December 2022
Floe Updates
v1.0.0 (Orion Release 2022.2)
Floe Updates
Deleted Floes
Cube Updates
v0.6.0 (Orion Release 2021.2)
Floe Updates
New Cubes
Cube Updates
v0.5.1 (Orion Release 2021.1)
New Floes
Floe Updates
New Cubes
Cube Updates
v0.4.0 (Orion Release 2020.3)
New Floes
Floe Updates
New Cubes
Cube Updates
Deleted Cubes
v0.3.0 (Orion Release 2020.2)
New Floes
Floe Updates
New Cubes
Cube Updates
v0.2.0 (Orion Release 2020.1)
General Notice
New Floes
Floe Updates
New Cubes
Cube Updates
Removed Cubes
Bibliography
Snowball - The Primary OpenEye Cube Library
Definitions of Floe Classifications
snowball - Cube Documentation
2D Depiction
Molecule Annotation
Molecule Depiction
Molecule Highlighting
Molecule Similarity Depiction
Property Depiction
Protein-Ligand Visualization
Shape and Color Overlap Visualization
Visualizing 3D Information
2D Similarity
2D Fingerprint
3D Similarity
Electrostatics
RMSD
Shape
Cheminformatics
Bemis Murcko Scoring
Mol Title from String Field
Rename A Field
Atom-Bond Typing
Atropisomerism
Dipole Moment Calculation
InChI
Maximum Common Substructure Search
Molecular Complexity
Molecular Descriptor
Molecule Alignment
Molecule Annotation and Tagging
Molecule Filtering
Molecule Manipulation
Molecule Naming
Molecule Processing
Molecule Property Calculation
SMILES
Substructure Search
Conformations
Conformer Manipulation
Debugging
Count Records
Log Record Fields
Examples
Index Generator
Floe Report
Brood Report Cube
Gameplan Report Cube
Brood
IO
Writers
Lead Optimization
Brood
Library Design
Apply ChEMBL Solubility Transformations
Ligand Modeling
EON
ForceField
Freeform Conf
Freeform Conf Advanced
Freeform Solv
Hermite
Kriging
PB-Electrostatics
Quacpac
ROCS
Ligand Preparation
Check for Partial Charges
Charging
OMEGA
Quacpac-prep
ROCS-prep
Szybki
Zap
Logic
Chunk
Classification
Field Conversion
Field Manipulation
Hit Lists
Numeric Comparison
Random Selection
Record Manipulation
String Comparison
Switches
MMDS
Data Load
Data Preparation
Models
Sorting Records by Index
ShapeQuery
Protein Ligand
Szybki
SiteHopper
Prep
Search
Spruce
Biomodeling
Format conversion
Structure Preparation
Structure Based Design
BintScore
Brood
Chemgauss4
Dock
Posit
Szmap
Surface
Invert Surface
Is Surface Open
Make Grid From Surface
Make Spherical Surface
Molecular Surface
Polar Surface Area
Rotate Surface
Smooth Surface
Split Surface By Atoms
Surface Area
Surface To Molecule Distance
Surface Volume
Transform Surface
Translate Surface
Unclassified
2D Fragment Picker
2D Torsion Picker
Add UUID Cube
Assign design unit partial charges
Bound Ligand Entropy
Brood Fragment Selector
Build 2D BROOD Database
Freeform Conf Restriction Energies
Generate Targets Mixin
MDL Query Editor
Macrocycle Filter Cube
Multistate pKaModel-based Ionization States Enumeration
Numeric Field To Constant Value Comparison
Read Structure Collection Mixin
Valence Screening Cube
Utility
Add Boolean Field
Add Design Unit Field
Add Query Style
Check Design Unit
Convert Conformers to Mols
Convert Shape Query to Record
Dataset Reader Optional
Dataset Size Router
Design Unit Exception Handler
Exception Handler
Failure Report
Failure Report
Field Type Conversion Cube
Find Ligand
Find Protein
Find Receptor
Find ShapeQuery
Loop Database File Look-up
Molecule Counter
Named Collection Reader
Named Dataset Reader
Named File Reader
Pass Query molecules to top of output
Pass Query to top of output
Process Every N records
Process N records
Protein Preparation Issues Detector
Protein Preparation Report
Shard Reader Optional
Single File Reader
String Parameter to String Field
Success Counter
Success Counter
Success Counter Shard
Release Notes
v0.28.0 July 2024
General Notice
New Cubes
Cube Updates
v0.27.0 February 2024
General Notice
New Cubes
Cube Updates
v0.26.1 September 2023
General Notice
v0.26.0 July 2023
General Notice
New Cubes
Cube Updates
v0.25.3 December 2022
General Notice
New Cubes
Cube Updates
v0.24.1 September 2022
General Notice
Cube Updates
v0.24.0 July 2022
General Notice
New Cubes
Cube Updates
v0.23.1 December 2021
General Notice
New Cubes
Cube Updates
Deprecated Cubes
v0.20.1 June 2021
New Cubes
Cube Updates
v0.20.1 November 2020
New Cubes
Cube Updates
v0.19.3 August 2020
Cube Updates
v0.19.1 August 2020
New Cubes
Cube Updates
Removed Cubes
v0.18.2 April 2020
General Notice
New Cubes
Cube Updates
Removed Cubes
v0.17.2 November 2019
General Notice
New Cubes
Cube Updates
v0.16.6 September 2019
General Notice
New Cubes
Cube Updates
v0.16.0 July 2019
General Notice
v0.15.0 June 2019
General Notice
v0.14.0 June 2019
General Notice
New Cubes
Cube Updates
v0.13.6 March 2019
General Notice
New Cubes
Cube Updates
v0.13.4 November 2018
General Notice
Cube Updates
v0.13.3 September 2018
General Notice
New Cubes
Cube Updates
v0.13.0 August 2018
General Notice
Crystal Structure Prediction & Properties
Theory
Crystal structure predictions
Random packing
Force field
Quantum Methods
Intrinsic Solubility
Tutorials
Crystal Structure Predictions using Crystal Math Floes
Introduction
Main Floes in the CSP Protocol
Additional Optional Floes
Crystal Math Floes - Documentation
Automated Force Field Solubility
Automated QM Solubility
CIF Reader
Cost Estimation for Crystal Structure Prediction
Crystal RMSD Deduplication Floe
Crystal RMSD Floe
Filtering of Crystal Structures Based on Powder Diffraction Pattern
Force Field Crystal Entropy with a Cluster Expansion Method
Force Field Optimization of Crystal Structures in the Dimer Expansion Approach
Loose Quantum Optimization of Crystal Structures (Part IIIA of CSP Protocol)
Polymorph Filtering Based on IEFF Energies (Part II’ of CSP Protocol: Filtering)
Polymorph Search with IEFF Crystal Force Field (Part II of CSP Protocol: Generation and Filtering)
Psi4 Combined Tautomer and Torsion Sampling Conformer Floe
Psi4 QM Conformer Ensemble (Part I of CSP Protocol)
QM Crystal Entropy with a Cluster Expansion Method (Part IV of CSP Protocol)
Quantum Optimization of Crystal Structures (Part IIIB of CSP Protocol)
Solubility from Crystal Entropy and Enthalpy
Water Sampling Floe
Release Notes
v2.9.2 December 2022
Required Dependency Changes
Floe Updates
v2.8.1 July 2022
General Notice
Floe Updates
v2.7.1 December 2021
General Notice
Floes in this package
Floe Updates
v2.5.0 November 2020
General Notice
New Floes
Floe Updates
v2.0.0 August 2020
General Notice
New Floes
Floe Updates
v1.8.4 April 2020
General Notice
Floe Updates
Bibliography
Gaussian Documentation
Gaussian Floe Tutorials
Introduction
Content of these Tutorials
Tutorial Data on Orion
Gaussian QM Conformer Ensemble Tutorial
Gaussian QM Torsion Scan Tutorial
Gaussian QM Run Input Files Successful Calculation
Locate and Run the Floe
Download and Analyze Results
Gaussian QM Run Input Files Failed Calculation
Understanding Failure Reports
Gaussian QM Single-Point Energy Tutorial
Gaussian QM Geometry Optimization Tutorial
Frequently Asked Questions
When should hardware requirements be changed?
How should hardware metrics be checked in QM calculations?
How much will a Floe cost?
What method and basis set should be used?
How can Gaussian log files be used to understand failures?
Why are there multiple serial cubes for running input files?
How do you create datasets on Orion?
Why are my calculations failing due to the presence of implicit hydrogens?
How do you rerun a Gaussian calculation from a checkpoint file?
Can GPUs be used with Gaussian on Orion?
How should files for the
Run Gaussian Input File Floe
be created and organized?
Why did the Gaussian input file change after running on Orion?
What should you know before running a large calculation with a Gaussian input file?
OpenEye Gaussian QM Floes - Documentation
Gaussian QM Conformer Ensemble
Gaussian QM Fragmentation and Torsion Scan
Gaussian QM Geometry Optimization
Gaussian QM Parallel Run Input Files
Gaussian QM Run Input Files
Gaussian QM SMARTS Torsion Scan
Gaussian QM Single Point Energy
Gaussian QM UI Torsion Scan
Release Notes
v0.5.0 July 2024
Floe Updates
v0.4.0 July 2023
New Floes
Floe Updates
v0.3.3 December 2022
Floe Updates
v0.2.0 (Orion Release 2022.2)
New Floes
Floe Updates
v0.1.0 (Orion Release 2022.1)
New Floes
New Cubes
3D Antibody Modeling Package
3D Antibody Modeling Tutorial
Floes Used in This Tutorial
Importing Sequences
Antibody Model Generation
Starting with Sequences
Starting with Experimental Structures
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
General Notice
Floe Updates
v0.1.3 April 2024
General Notice
Bibliography
AbXtract™ - NGS Antibody Discovery
Introduction to AbXtract
Tutorials
Tutorial 1: NGS Pipeline with Custom Interactive Selection (PacBio), In-Vitro Library
Background
STEP 1 - Log in to Orion, Set Up Directory, Locate Tutorial Files
STEP 2 - Select the ‘NGS Pipeline’ Floe
STEP 3 - Prepare PacBio Run and Start Job
STEP 4 - Open the Floe Report to Get a General Idea About the Population
STEP 5 - Activate the Dataset
STEP 6 - Plot Relative Abundance Versus Desired Overlap Population and Select Population with Analyze Tool
STEP 7 - Select the Enriched Population Using the Analyze Tool and Send to the Automated Top Lead Selection Floe
STEP 8 - Subset the Number of Fields for Output and Download CSV
Tutorial 2: NGS Pipeline with Automated Top Lead Selection (PacBio), In-Vitro Library
Background
STEP 1 - Login to Orion, Set-Up Directory, Locate Tutorial Files
STEP 2 - Select the ‘NGS Pipeline with Automated Lead Selection’ Floe
STEP 3 - Prepare PacBio Run and Start Job
STEP 4 - Open the Floe Report to Get a Detailed Understanding of the Selected or ‘Picked’ Population
STEP 5 - Select Populations with Net Negative Charge of the CDRs
STEP 6 - Subset the Output Fields
STEP 7 - Download the CSV
Tutorial 3: NGS and Sanger Pipeline with Automated Top Lead Selection (PacBio), In-Vitro Library
Background
STEP 1 - Login to Orion, Set-Up Directory, Locate Tutorial Files
STEP 2 - Select the ‘NGS and Sanger Pipeline with Automated Top Lead Selection’ Floe
STEP 3 - Prepare Sanger Files
STEP 4 - Prepare PacBio Files and Start Job
STEP 5 - Open the Floe Report to Get a Detailed Understanding of the Selected or ‘Picked’ Population
STEP 6 - Subset NGS Only Population by Cluster and Overlap_Population
Tutorial 4: NGS and Sanger Pipeline with Automated Top Lead Selection (Illumina), In-Vitro Library
Background
STEP 1 - Login to Orion, Set-Up Directory, Upload Files
STEP 2 - Select the ‘NGS and Sanger Pipeline with Automated Top Lead Selection’ Floe
STEP 3 - Prepare Sanger Files
STEP 4 - Prepare Illumina Files and Start Job
Tutorial 5: NGS Pipeline with Automated Top Lead Selection (PacBio), Patient Library
Background
STEP 1 - Login to Orion, Set-Up Directory, Upload Files
STEP 2 - Select the ‘NGS Pipeline with Automated Lead Selection’ Floe
STEP 3 - Prepare PacBio Run and Start Job
STEP 4 - Select Different Clonotyping Method
STEP 5 - Identify both the Picked and the Downstream Population
Tutorial 6: NGS UMIs Extract and Annotation Floe
Background
STEP 1 - Login to Orion, Set-Up Directory, Upload Files
STEP 2 - Select the ‘NGS Pipeline with Automated Lead Selection’ Floe
STEP 3 - Prepare PacBio Run and Start Job
STEP 4 - Select Different Clonotyping Method
STEP 5 - Identify both the Picked and the Downstream Population
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
What is the difference between upstream and downstream chain designations, _1 and _2?
What is the difference between upstream and downstream AbXtract floe processing?
What input formats do the AbXtract upstream processing floes accept, and what are the requirements?
What is the region of interest (ROI)?
Where are the liabilities tabulated in AbXtract?
There are several overlap options available. What are the differences among the different overlap options?
What input formats do the AbXtract downstream processing floes accept, and what are the requirements?
How many sequences can the platform process, and what is the output?
Why is the number of picked representatives below the total number of full-length when using the
Automated Top Lead Selection
Floe?
The clustering is taking quite a while with my inputs. Is there a way to bypass clustering in the
NGS (PacBio/Illumina) Pipeline
Floe?
I do not need the Floe Report. Can I bypass this option?
What is a barcode file, barcode_group, barcode_round, and sample_name? How do you format this table?
What is a customized DNA or AA Database?
How is relative enrichment calculated?
How is relative abundance calculated?
What is meaning of the cluster vocabulary? What is a cluster? What is the difference between cluster and cluster_numeric?
I have selected the Levenshtein or Hamming Distance Clustering Method. Where do I modify the edit distance?
How are liabilities quantified, and what do the different liability fields mean?
What is a customized liabilities table/database, how is it formatted, and does it override the floe parameters?
How many records are typically handled by the Analyze tool?
How long does it take to load the Floe Report? Where in Orion can the Floe Reports be found?
I am having difficulty uploading my FASTQ file or Orion logs out before process is complete, how do I overcome this?
Why is my download taking so long?
My floe fails due to a memory allocation issue. How do I overcome this?
My floe is stalling for more than 48 hours in the
NGS (PacBio/Illumina) Pipeline
Floe, or beyond the cost level acceptable for this job?
What happens if I want to change a barcode group after the FASTQ has already been processed or I did not add a barcode group?
I am having difficulty downloading my file from the dropdown option for my given dataset?
I processed an AIRR-compatible file and want to link the AbXtract values to the original input values. How can I do that?
Will annotating my sequences using the
NGS (PacBio/Illumina) IgMatcher, Annotation Only - AbXtract
Floe give me the same result as my AIRR-compatible file?
Why are there twice as many records/rows output when I convert a PacBio input to an AIRR-compatible file?
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
abxtract - Cube Documentation
AbXtract, Liabilities
AbXtract, Sanger
AbXtract - Biophysical
Sequence-Based Biophysical Sequence Calculation
AbXtract - Downstream Processing
AbXtract Processing, NGS Only
AbXtract Processing, NGS and SANGER
Binary Enrichment and Relative Abundance Calculation
Binary Input to Cluster
Binary Liability Calculation
Clustering by AbScan, Edit Distance, or 100% Homology
Condense Total Number of Sequences by Region of Interest (ROI)
Enrichment and Depletion Tracing of Clones
Enrichment and Relative Abundance Calculation
Export AIRR fields for dataset
Liabilities Quantification
Liabilities Quantification, Improved
Overlap Among Different NGS Barcode Populations
AbXtract - SANGER Processing
Inputting SANGER File (Excel, TSV, CSV)
Inputting SANGER File (Excel, TSV, CSV)
Inputting SANGER File (Excel, TSV, CSV) - BETA
Inputting SANGER Records - BETA
OE Sanger Assembly
OE Sanger Assembly P
OE Sanger Read Pairing
Write Consolidated AbXtract Dataset
AbXtract - Upstream Processing
Input File from NovaSeq
Inputting FASTQ for Illumina
Inputting FASTQ for Illumina
Inputting FASTQ for Illumina
Inputting FASTQ for PacBio
Inputting FASTQ for PacBio with Compressed Files
Inputting FASTQ for PacBio with Compressed Files
NovaSeq Binary Handler
Sequence Annotation with IgMatcher for Illumina
Sequence Annotation with IgMatcher for PacBio
Sequence Annotation with IgMatcher for PacBio
Automated Lead Selection
Custom Select NGS Leads by Sequence ID with File
Select NGS Leads Matching SANGER
Select X Number of Non-Redundant Sequences by Cluster or ROI
Select X Number of Non-Redundant Sequences by Cluster or ROI
Select X Number of Non-Redundant Sequences by Cluster or ROI
Write Consolidated AbXtract Dataset
Write Consolidated AbXtract Dataset
Write Consolidated AbXtract Dataset
Converting dataframe to blob.
Loads Cluster Assignment by Region of Interest
RecordToDataFrameBlob
Write Top Ranked Clusters
Long-Read
Full-Chain
Unclassified
Read Collections and Condense Data
Read Collections and Condense Data
Reads in Collection and Output Individual Record
Record Field Initializer Cube
Upload, Modify or Subset
Modify Sample Name or Barcode Group in AbXtract Dataset
Subset AbXtract Fields
Upload AbXtract Compatible File
Writing Reports and Datasets
Consolidating and Writing Datasets
Consolidating and Writing Datasets, Illumina
Consolidating and Writing Datasets, PacBio
Consolidating and Writing Datasets, Sanger
Long or Short-Read Sequence Identifier
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
General Notice
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Sample Code
Citation
Orion
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Toolkits and Applications
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Technology Licensing
GCC
GCC RUNTIME LIBRARY EXCEPTION
GNU GENERAL PUBLIC LICENSE
Suites and Modules User Guide
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CCDC GOLD Orion Integration User Guide
CCDC GOLD Orion Integration User Guide
¶
https://www.ccdc.cam.ac.uk/media/Orion-GOLD-User-guide.pdf