OEApplications 2024.1
Release Highlights 2024.1.3
Release Highlights 2024.1.0
EON: Overlay Optimization with Shape and Charge Density
FLYNN: Ligand fitting for Cryo-EM
Hydrogen Placement Updates in
SPRUCE
Bioisostere TK: New Toolkit for Bioisosteric Fragment Replacement
Supported Platforms
Related Application Versions
Detailed Release Notes 2024.1
AFITT 3.0.0
New Features
BROOD 4.0.0
Major bug fixes
Bioisostere TK 4.0.0
New features
EON 3.0.0.3
EON 3.0.0.0
New Features
Zap TK 2.4.7
OEDocking 4.3.1
OEDocking TK 4.3.1.3
OEDocking TK 4.3.1.0
OMEGA 5.1.0
New Features
Major bug fixes
Omega TK 5.1.0
New features
Minor bug fixes
MolProp TK 2.6.4
PICTO 5.1.1
OEDepict TK 2.5.4
pKa-Prospector 1.2.3
QUACPAC 2.2.4
Quacpac TK 2.2.3
ROCS 3.6.2
New Features
Major bug fixes
Minor bug fixes
Shape TK 3.6.2
New features
SiteHopper 2.1.0
SiteHopper TK 2.1.0
New features
SPRUCE 1.6.0
Spruce TK 1.6.0
New features
Major bug fixes
Minor bug fixes
Documentation changes
SZMAP 1.7.0
Minor bug fixes
Szmap TK 1.7.0
Documentation changes
SZYBKI 2.7.1
Szybki TK 2.7.1.3
Szybki TK 2.7.1.0
VIDA 5.0.6
Previous Release Highlights
Release Highlights 2023.2.3
Supported Platforms
Related Application Versions
Release Highlights 2023.1.1
Release Highlights 2023.1.0
Supported Platforms
Related Application Versions
Release Highlights 2022.2.2
Release Highlights 2022.2.1
MCS based fix during OMEGA Conformer Generation
New ShapeFit Algorithm for Pose Prediction
Protein-ligand Optimization with ff14SB forcefield and PB solvent model
New
BROOD
Fragment Databases
Supported Platforms
Related Application Versions
General Notices
Release Highlights 2022.1
Enhanced Stereo Information Support
Sheffield Solvation Model for Proteins
Spruce Filter and Design Unit Validation
Multistate Heuristic pKa Model
Supported Platforms
Related Application Versions
General Notices
Release Highlights 2021.2
SiteHopper: New Toolkit for Protein Binding Site Comparison
SZYBKI: OpenFF-Sage force field support
OEChem: MMCIF and CIF writers
Supported Platforms
Related Application Versions
General Notices
Release Highlights 2021.1
OESiteHopper: Application Suite for Rapid Protein Binding Site Comparison
OEDocking: MakeReceptor (Receptors in Design Unit)
VIDA 5: Major Update and OEDesignUnit support
Supported Platforms
Related Application Versions
General Notices
Release Highlights 2020.2.2
Release Highlights 2020.2
OMEGA: New fragment library
OEDOCKING: Improved receptors
SZYBKI: A new protein force field
Supported Platforms
Related Application Versions
General Notices
Release Highlights 2020.1.1
Release Highlights 2020.1
Release Highlights 2020.0
OMEGA: GPU-OMEGA - GPU-accelerated torsion driving
SPRUCE: Protein Loop Modeling
SZYBKI: Custom SMIRNOFF
General Notices
Release Highlights 2019.Nov
SPRUCE: Application Suite for Biomolecular Structure Preparation
SZMAP: Simplified Workflow
SZYBKI: SMIRNOFF
General Notices
Platform Support
Release Highlights 2019.May
Windows Installer
OEZ Compressed File Format
General Notices
Platform Support
OEApplications 2018.Nov
First release of all OpenEye Applications as a single package
ROCS: ROCS
QUACPAC: Tautomers
General Notices
Platform Support
Getting Started
Installation and Platform Notes
Licenses for OpenEye Software
Installation
Example and Tutorial Data
MPI
Uninstallation
Release Cycle
Legal Notices
Copyright and Trademarks
Sample Code
Citation
Technology Licensing
AFITT 3.0.0.3
Overview
Applications
Utility Programs
FLYNN
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Usage Notes
Coot Integration
Overview
Using FLYNN
Using WriteDict
Using RotFit
Installing Coot Interface
Utilities
AlignGrid
RotFit
Rscc
WriteDict
Theory
Fragment Fitting
Release History
AFITT 3.0.0
AFITT 2.6.5
AFITT 2.6.4
AFITT 2.6.3
AFITT 2.6.2
AFITT 2.6.1
AFITT 2.6.0
AFITT 2.5.3
AFITT 2.5.2.0
AFITT 2.5.1
AFITT 2.5.0
AFITT-CL 2.4.1
AFITT-CL 2.4.0
AFITT-CL 2.3.0
AFITT-CL 2.2.0
AFITT-CL 2.1.1
AFITT-CL 2.1.0
AFITT-CL 2.0.1
FLYNN 2.0.0
Citation
BROOD 4.0.0.3
Introduction
Applications
Utility Programs
Installing the BROOD Database
vBROOD
Overview
Build and Run
Build a New Query
Run BROOD
Filtering
View Results
Viewing Results in VIDA
BROOD
Overview
Input Files
Example Commands
Command Line Help
Parameters
Output Files
CHOMP
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Utilities
Overview
Command Line Help
Example Commands
Required Parameters
Optional Parameters
Overview
Human Complement C3a Receptor Example
Specifying the database
Loading a molecule
Editing the query
Selecting properties
Setting up the BROOD search
Opening and viewing results
Exploring the Results
Fragment Joining Tutorial
BROOD database
Loading two molecules
Loading the protein
Choosing a query
Setting up a search
Examining the Log files
Viewing results in a protein site
Generating a Database with Crystallographic Conformations
Preparing data sources
Generating a database
Advanced topic: editing the fragments at an intermediate step
Theory
Theory
Fragment joining
Cyclization
BROOD Database Generation (CHOMP)
BROOD Fragment Database
ChEMBL31 Fragment Database
ChEMBL31_lite Fragment Database
brood-database-chembl-3.0.0
Release History
BROOD 4.0.0
Bioisostere TK 4.0.0
BROOD 3.2.2
BROOD 3.2.1
BROOD 3.2.0
BROOD 3.1.7
BROOD 3.1.6
BROOD 3.1.5
BROOD 3.1.4.0
BROOD 3.1.3
BROOD 3.1.2
BROOD 3.1.1
BROOD 3.1.0
BROOD 3.0.0
BROOD 2.0.0
BROOD 1.1.2
BROOD 1.1.1
BROOD 1.1.0
BROOD 1.0.1
BROOD 1.0.0
BROOD 0.9.b2
BROOD 0.9.b1
Citation
EON 3.0.0.3
Introduction
Overview
Applications
EON
Overview
Example Commands
Report File
Command Line Help
Required Parameters
Optional Parameters
Theory
Release History
EON 3.0.0.3
EON 3.0.0.0
Zap TK 2.4.7
EON 2.4.2
Zap TK 2.4.6
EON 2.4.1
Zap TK 2.4.5
EON 2.4.0
Zap TK 2.4.4
EON 2.3.7
Zap TK 2.4.3
EON 2.3.6
Zap TK 2.4.2
EON 2.3.5
Zap TK 2.4.1
EON 2.3.4.0
Zap TK 2.4.0
EON 2.3.3
EON 2.3.2
EON 2.3.1
EON 2.3.0
EON 2.2.0
EON 2.1.0
EON 2.0.0
Citation
OEDocking 4.3.1.3
Introduction
Overview
Applications
Utility Programs
Tutorials
Overview
Receptor preparation tutorial
CombineReceptors tutorial
FRED tutorial
HYBRID tutorial
POSIT tutorial
POSIT MPI tutorial
Theory
Receptors
FRED Theory
HYBRID Theory
Scoring Functions
POSIT Theory
Posit How to
FRED
Overview
Input Preparation
Example Commands
Command Line Help
Required Parameters
Optional Parameters
HYBRID
Overview
Input Preparation
Example Commands
Command Line Help
Required Parameters
Optional Parameters
POSIT
Overview
Input Preparation
Example Commands
Command Line Help
Required Parameters
Optional Parameters
MakeReceptor
Overview
GUI Layout
Setting up a Receptor
Utilities
ReceptorInDU
OEB2DUReceptor
DockingReport
ScorePose
ReceptorToolbox
combine_receptors
DU2OEBReceptor
Release History
OEDocking 4.3.1
OEDocking TK 4.3.1.3
OEDocking TK 4.3.1.0
OEDOCKING 4.3.0
OEDocking TK 4.3.0
OEDOCKING 4.2.1.1
OEDOCKING 4.2.1.0
OEDocking TK 4.2.1
OEDOCKING 4.2.0
OEDocking TK 4.2.0
OEDOCKING 4.1.2
OEDocking TK 4.1.2
OEDOCKING 4.1.2
OEDocking TK 4.1.2
OEDOCKING 4.1.0
OEDocking TK 4.1.0
OEDOCKING 4.0.0.2
OEDOCKING 4.0.0.0
OEDocking 3.5.0
OEDocking 3.4.0
OEDocking 3.3.1
OEDocking 3.3.0
OEDocking 3.2.0
OEDocking 3.0.1
OEDocking 3.0.0
POSIT 3.1.0
POSIT 1.0.3
POSIT 1.0.2
POSIT 1.0.1
POSIT 1.0.0
FRED 2.2.5
FRED 2.2.4
FRED 2.2.3
FRED 2.2.2
FRED 2.2.1
FRED 2.2.0
Citation
OMEGA 5.0.1.3
Introduction
Overview
Applications
Utility Programs
FILTER
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Filter Files
OMEGA
Overview
GPU-Omega
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Additional specifications
Utilities
Flipper
MakeFraglib
Oeb2SdConf
Theory
OMEGA Theory
Macrocycle Conformations
Filtering Theory
Release History
OMEGA 5.1.0
Omega TK 5.1.0
MolProp TK 2.6.4
OMEGA 5.0.0
Omega TK 5.0.0
MolProp TK 2.6.3
OMEGA 4.2.2
Omega TK 4.2.2
MolProp TK 2.6.2
OMEGA 4.2.1
OMEGA 4.2.0
Omega TK 4.2.0
MolProp TK 2.6.0
OMEGA 4.1.2
Omega TK 4.1.2
MolProp TK 2.5.7
OMEGA 4.1.1
Omega TK 4.1.1
MolProp TK 2.5.6
OMEGA 4.1.0.0
Omega TK 4.1.0
MolProp TK 2.5.5
OMEGA 4.0.0.6
OMEGA 4.0.0
OMEGA 3.1.2
OMEGA 3.1.1
OMEGA 3.1.0
OMEGA 3.0.1
OMEGA 3.0.0
OMEGA 2.5.1
OMEGA 2.4.6
OMEGA 2.4.3
OMEGA 2.4.1
OMEGA 2.4.0
OMEGA 2.3.3
OMEGA 2.3.2
OMEGA 2.3.1
OMEGA 2.3.0
OMEGA 2.2.2
OMEGA 2.2.1
Citation
PICTO 5.1.1.3
Introduction
Overview
Applications
PICTO
Overview
Sketcher
SMARTS
Implicit/Explicit Hydrogens
Atom Labeling, Aromatic Displays, Aromatic Modeling, and other Displays
Release History
PICTO 5.1.1
OEDepict TK 2.5.4
PICTO 5.1.0
OEDepict TK 2.5.3
PICTO 4.6.0
OEDepict TK 2.5.1
PICTO 4.5.4
OEDepict TK 2.5.0
PICTO 4.5.3
OEDepict TK 2.4.7
PICTO 4.5.2
OEDepict TK 2.4.6
PICTO 4.5.1.0
OEDepict TK 2.4.5
PICTO 4.5.0
Citation
pKa-Prospector 1.2.3.3
Introduction
Overview
Applications
pKa-Prospector
Overview
QuickStart
Query Molecule
Property Filters
Search Buttons
Results View
Preferences
Result Report
Menu Items
Appending Data
Selecting an Imported Database
Release History
pKa-Prospector 1.2.3
pKa-Prospector 1.2.2
pKa-Prospector 1.2.1
pKa-Prospector 1.2.0
pKa-Prospector 1.1.7
pKa-Prospector 1.1.6
pKa-Prospector 1.1.5
pKa-Prospector 1.1.4.0
pKa-Prospector 1.1.3
pKa-Prospector 1.1.2
pKa-Prospector 1.1.1
pKa-Prospector 1.1.0
pKa-Prospector 1.0.0
Citation
QUACPAC 2.2.4.3
Introduction
Overview
Applications
FixpKa
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
MolCharge
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
pKaTyper
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Tautomers
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
MolCharge Theory
Introduction
Marsili-Gasteiger Partial Charges
MMFF94 Partial Charges
AM1 Charges
AM1BCC Charges
ELF Conformer Selection
Amber ff94, ff96, ff99, ff99sb, and ff99sbc0 Partial Charges
Release History
QUACPAC 2.2.4
Quacpac TK 2.2.3
QUACPAC 2.2.3
Quacpac TK 2.2.3
QUACPAC 2.2.2
Quacpac TK 2.2.2
QUACPAC 2.2.1
Quacpac TK 2.2.1
QUACPAC 2.2.0
Quacpac TK 2.2.0
QUACPAC 2.1.3
Quacpac TK 2.1.3
QUACPAC 2.1.2
Quacpac TK 2.1.2
QUACPAC 2.1.1.0
Quacpac TK 2.1.1.2
Quacpac TK 2.1.1
QUACPAC 2.1.0
QUACPAC 2.0.2
QUACPAC 2.0.1
QUACPAC 2.0.0
QUACPAC 1.7.0
QUACPAC 1.6.3
QUACPAC 1.5.0
QUACPAC 1.3.1
QUACPAC 1.3.0
QUACPAC 1.1.0
molcharge
Appendix: Complete list of
-method
options
Citation
ROCS 3.6.2.3
Introduction
Overview
Applications
Utility Programs
ROCS
Overview
Input Files
Example Commands
Report File
Command Line Help
Required Parameters
Optional Parameters
vROCS
Overview
Setup a simple run and a validation run
Results visualization and analysis
Statistics metrics
Saving ROCS data
ROCS shape query sources
Editing ROCS queries in vROCS
vROCS menus
Utilities
CheckCff
Chunker
HLMerge
MakeRocsDB
ROCSReport
ROCS Tutorials
Introduction
Build/edit a query using the Wizard
Build/edit a query manually
Perform a ROCS validation run
Perform a simple ROCS run
Perform a ROCS run from the command line
Theory
Shape Theory
Color Features
Color Force Field
Similarity Measures
Release History
ROCS 3.6.2
Shape TK 3.6.2
ROCS 3.6.1
Shape TK 3.6.1
ROCS 3.6.0
Shape TK 3.6.0
ROCS 3.5.1
Shape TK 3.5.1
ROCS 3.4.3
Shape TK 3.4.3
ROCS 3.4.2
Shape TK 3.4.2
ROCS 3.4.1.0
Shape TK 3.4.1
ROCS 3.4.0
ROCS 3.3.2
ROCS 3.3.1
ROCS 3.3.0
ROCS 3.2.2
ROCS 3.2.1
ROCS 3.2.0
ROCS 3.1.2
ROCS 3.1.1
ROCS 3.1.0
ROCS 3.0.0
ROCS 2.4.2
ROCS 2.4.1
ROCS 2.3.1
ROCS 2.3.0
ROCS 2.2.0
List of selected ROCS publications
Citation
SiteHopper 2.1.0.3
Introduction
Overview
Applications
SiteHopper Search
Overview
GPU Prerequisites
Example Commands
Command Line Help
Required Parameters
Optional Parameters
SiteHopper build
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Release History
SiteHopper 2.1.0
SiteHopper TK 2.1.0
SiteHopper 2.0.4
Sitehopper TK 2.0.4
SiteHopper 2.0.3
Sitehopper TK 2.0.3
SiteHopper 2.0.2
Sitehopper TK 2.0.2
SiteHopper 2.0.1
Sitehopper TK 2.0.1
SiteHopper 2.0.0
SiteHopper TK 2.0.0
SiteHopper 1.0.0
Citation
SPRUCE 1.6.0.3
Introduction
Overview
Applications
Utility Programs
Utilizing a Loop Template Database
SPRUCE
Overview
Spruce Output Naming Conventions
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Superposition
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
EnumSites
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
GetStructure
Overview
Example Commands
LoopDBBuilder
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
DU2PDB
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
du2mmcif
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Release History
SPRUCE 1.6.0
Spruce TK 1.6.0
SPRUCE 1.5.3
Spruce TK 1.5.3
SPRUCE 1.5.2.1
SPRUCE 1.5.2.0
Spruce TK 1.5.2
SPRUCE 1.5.1
Spruce TK 1.5.1
SPRUCE 1.5.0
Spruce TK 1.5.0
SPRUCE 1.4.0
Spruce TK 1.4.0
SPRUCE 1.3.0
Spruce TK 1.3.0
SPRUCE 1.2.0.2
SPRUCE 1.2.0.0
Spruce TK 1.2.0
SPRUCE 1.1.0
SPRUCE 1.1.0
SPRUCE 1.0.0
Citation
SZMAP 1.7.0.3
Introduction
Overview
Applications
Utility Programs
A Word About Pronunciation
Spruce Before Szmap
Overview
SZMAP
Overview
SZMAP Input and Output
Example Commands
Command Line Help
Required Parameters
Optional Parameters
GamePlan
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Utilities
SzmapGrid
GridComp
SzmapReport
VIDA Extensions
Introduction
Installing VIDA Extensions
WaterColor VIDA Extension
Water Orientation VIDA Extension
Color By Atom Properties
Tutorials
SZMAP Workflow
Protein and Ligand Preparation
Running SZMAP Stabilization Calculations
Analyzing SZMAP Results
Running SZMAP at Coordinates
Running Gameplan
Theory
Philosophy and Design
Technical Details
Release History
SZMAP 1.7.0
Szmap TK 1.7.0
SZMAP 1.6.7
SZMAP 1.6.6
SZMAP 1.6.5
Szmap TK 1.6.5
SZMAP 1.6.4
Szmap TK 1.6.4
SZMAP 1.6.3
Szmap TK 1.6.3
SZMAP 1.6.2
Szmap TK 1.6.2
SZMAP 1.6.1.0
Szmap TK 1.6.1
SZMAP 1.6.0
SZMAP 1.5.0
SZMAP 1.4.1
SZMAP 1.4.0
SZMAP 1.3.0
SZMAP 1.2.1
SZMAP 1.2.0
SZMAP 1.1.1
SZMAP 1.1.0
SZMAP 1.0.0
Appendix 1: SZMAP Grids
Protein + Ligand Complex
Ligand Only
Protein Only
(Complex - Protein - Ligand) Stabilization
Appendix 2: SZMAP Atom Properties
Complex, Apo or Ligand
(Complex - Protein - Ligand) Stabilization
Citation
SZYBKI 2.7.1.3
Overview
Applications
Utility Programs
SZYBKI
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
FREEFORM
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Theory
SZYBKI Theory
Freeform Theory
Utilities
OptLigandInDU
OptimizeDU
Release History
SZYBKI 2.7.1
Szybki TK 2.7.1.3
Szybki TK 2.7.1.0
SZYBKI 2.7.0
Szybki TK 2.7.0
SZYBKI 2.6.0
Szybki TK 2.6.0.1
Szybki TK 2.6.0.0
SZYBKI 2.5.1
Szybki TK 2.5.1.2
Szybki TK 2.5.1.1
SZYBKI 2.5.0
Szybki TK 2.5.0
SZYBKI 2.4.0
SZYBKI 2.3.1
Szybki TK 2.3.1
SZYBKI 2.3.0.2
SZYBKI 2.3.0.0
Szybki TK 2.3.0
SZYBKI 2.2.0
SZYBKI 1.11.0
SZYBKI 1.10.1
SZYBKI 1.10.0
SZYBKI 1.9.0
SZYBKI 1.8.0
SZYBKI 1.7.0
SZYBKI 1.5.2
SZYBKI 1.5.1
SZYBKI 1.5.0
SZYBKI 1.3.4
SZYBKI 1.3.3
SZYBKI 1.3.2
SZYBKI 1.3.1
SZYBKI 1.3.0
SZYBKI 1.2.2
Citation
VIDA 5.0.6.3
Introduction
General Concepts
Scope
Layout
Undo / Redo
Mouse Map
User Directory
Help
Installation and Platform Notes
Enterprise Installation for Windows
File I/O
Opening Files
Closing Files
Saving Files
Importing Files
Exporting Files
Drag and Drop
Copy and Paste
3D Display
User Interaction
Rendering
Stereo
Viewpoint
Bookmarks
Tiled Display
Toolbars
Display Widgets
Molecular Visualization
Grid Visualization
Grid Types
Reentrant Grids
Surface Visualization
Symmetry
2D Display
Preview vs. Viewer
Interaction
Advanced Depiction Options
Spreadsheet
Basic Usage
Sorting
Displaying Data
Organizing Columns
Creating New Columns
Filtering
Statistics
Formatting Columns
Advanced Depiction Options
Importing/Exporting
Atom Spreadsheet
Residue Spreadsheet
List Management
Introduction
Browsing
Views
List Columns
List Manipulation
Processes
Processes
Pipes
Molecule Manipulation
Creating Molecules
Editing Molecules
Custom Views
FRED View
EON View
ROCS View
Selection Language
Introduction
Operators
Lists and Ranges
Properties
Macros/Pre-defined sets
Scripting with ScratchScope
Scripting
Journal File
Startup File
Scripts Directory
Scripting API
Scripting Window
OpenEye Toolkits
Customizing the User Interface
Extensions
Example Extensions
Extension Manager
Creating Extensions
Distributing Extensions
Preferences
Menus
File
Edit
View
Data
Style
Bookmarks
Tools
Select
Window
Help
Examples
Data
Scripts
VIDA Python API
General Functions
Scope Functions
User Interface Functions
Display Functions
Object Functions
Molecule Builder Functions
Data Analysis Functions
Deprecated Functions
Release History
VIDA 5.0.6
VIDA 5.0.5
VIDA 5.0.4
VIDA 5.0.3
VIDA 5.0.2
VIDA 5.0.1
VIDA 5.0.0
VIDA 4.4.0
VIDA 4.3.0
VIDA 4.2.0
VIDA 4.1.1
VIDA 4.1.0
VIDA 4.0.3
VIDA 4.0.0
VIDA 3.0.0
VIDA 2.1.2
VIDA 2.1.1
VIDA 2.1.0
VIDA 2.0.2
Citation
OpenEye Glossary of Terms
Bibliography
Applications-
All OpenEye Documentation
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Contents
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pKa-Prospector 1.2.3.3
»
Release History
»
pKa-Prospector 1.2.0
pKa-Prospector 1.2.0
ΒΆ
Fall 2022
Minor internal improvements have been made.