OEApplications 2025.1.1
Highlights of Applications Release 2025.1
FastROCS: Grid Query Support
Bioisostere TK: Feature Extensions
SZYBKI: Robust Protein–Ligand Optimization
Supported Platforms
Related Application Versions
Detailed Release Notes 2025.1
AFITT
BROOD
EON
OEDOCKING
OMEGA
PICTO
PKA-PROSPECTOR
QUACPAC
ROCS
SITEHOPPER
SPRUCE
SZMAP
SZYBKI
Previous Release Highlights
Release Highlights 2024.2.1
Release Highlights 2024.2.0
Supported Platforms
Related Application Versions
Release Highlights 2024.1.3
Release Highlights 2024.1.0
Supported Platforms
Related Application Versions
Release Highlights 2023.2.3
Release Highlights 2023.1.1
Release Highlights 2023.1.0
Release Highlights 2022.2.2
Release Highlights 2022.2.1
Release Highlights 2022.1
Release Highlights 2021.2
Release Highlights 2021.1
Release Highlights 2020.2.2
Release Highlights 2020.2
Release Highlights 2020.1.1
Release Highlights 2020.1
Release Highlights 2020.0
Release Highlights 2019.Nov
Release Highlights 2019.May
OEApplications 2018.Nov
Applications
Getting Started
Installation and Platform Notes
Release Cycle
Legal Notices
AFITT 3.0.2.1
Overview
Applications
Utility Programs
FLYNN
Coot Integration
Utilities
Theory
Release History
Citation
BROOD 4.2.0.1
Introduction
vBROOD
BROOD
CHOMP
Utilities
Overview
Human Complement C3a Receptor Example
Fragment Joining Tutorial
Generating a Database with Crystallographic Conformations
Theory
BROOD Fragment Database
Release History
Citation
EON 3.1.1.1
Introduction
EON
Theory
Release History
Citation
OEDocking 4.3.3.1
Introduction
Tutorials
Theory
FRED
HYBRID
POSIT
Make Receptor
Utilities
Release History
Citation
OMEGA 6.1.0.1
Introduction
FILTER
OMEGA
Utilities
Theory
Release History
Citation
PICTO 5.1.3.1
Introduction
PICTO
Release History
Citation
pKa-Prospector 1.2.5.1
Introduction
pKa-Prospector
Release History
Citation
QUACPAC 2.2.6.1
Introduction
FixpKa
MolCharge
pKaTyper
Tautomers
MolCharge Theory
Release History
molcharge
Appendix: Complete list of
-method
options
Citation
ROCS 3.8.0.1
Introduction
ROCS
vROCS
Utilities
ROCS Tutorials
Theory
Release History
List of selected ROCS publications
Citation
SiteHopper 2.1.2.1
Introduction
SiteHopper Search
SiteHopper build
Release History
Citation
SPRUCE 1.7.0.1
Introduction
SPRUCE
Superposition
EnumSites
GetStructure
LoopDBBuilder
DU2PDB
du2mmcif
Release History
Citation
SZMAP 1.7.2.1
Introduction
Spruce Before Szmap
SZMAP
GamePlan
Utilities
VIDA Extensions
Tutorials
Theory
Release History
Appendix 1: SZMAP Grids
Appendix 2: SZMAP Atom Properties
Citation
SZYBKI 2.9.0.1
Overview
Applications
Utility Programs
SZYBKI
FREEFORM
Theory
Utilities
Release History
Citation
VIDA 5.0.7.2
Introduction
Installation and Platform Notes
File I/O
3D Display
2D Display
Spreadsheet
List Management
Processes
Molecule Manipulation
Custom Views
Selection Language
Scripting
Extensions
Preferences
Menus
Examples
VIDA Python API
Release History
Citation
OpenEye Glossary of Terms
Bibliography
Applications-
All OpenEye Documentation
»
Contents
»
Applications
»
AFITT 3.0.2.1
AFITT 3.0.2.1
¶
Overview
Applications
Utility Programs
FLYNN
Overview
Example Commands
Basic Usage
Generating Reports
Choosing box regions of density
Choosing density close to residues
Choosing MTZ columns
Fragment usage
Command Line Help
Required Parameters
Optional Parameters
Input Options
MTZ File Options
Advanced Options
Fragment Fitting Options
3D Construction Options
Usage Notes
Minimum Requirements
Types of input ligands
Stereochemistry Enumeration
Refinement Dictionaries
REFMAC5 refinement dictionaries
Looking up known residues
MMFF94 versus MMFF94s forcefields
FLYNN and writing CIF Files
Results on The Gold Test Set
Coot Integration
Overview
Using FLYNN
FLYNN Advanced Options
Using WriteDict
WriteDict Advanced Options
planarAniline option
Using RotFit
ROTFIT options
Installing Coot Interface
Coot
WinCoot 0.9.4.1+
WinCoot 0.3.3 to 0.8.9.2
Utilities
AlignGrid
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
RotFit
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Rscc
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
WriteDict
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Theory
Fragment Fitting
Release History
FLYNN 3.0.2
AFITT 3.0.1
AFITT 3.0.0
New Features
AFITT 2.6.5
AFITT 2.6.4
AFITT 2.6.3
AFITT 2.6.2
AFITT 2.6.1
AFITT 2.6.0
New features
AFITT 2.5.3
Minor Bug Fixes
Documentation Changes
AFITT 2.5.2.0
AFITT 2.5.1
AFITT 2.5.0
AFITT-CL 2.4.1
Platform Support
Coot Support
Bug Fixes
AFITT-CL 2.4.0
Platform Support
FLYNN
WRITEDICT
ROTFIT
AFITT-CL 2.3.0
Other
WRITEDICT
FLYNN
COOT Integration
AFITT-CL 2.2.0
WRITEDICT
FLYNN
AFITT-CL 2.1.1
WRITEDICT
FLYNN
AFITT-CL 2.1.0
WRITEDICT
FLYNN
AFITT-CL 2.0.1
WRITEDICT
FLYNN
FLYNN 2.0.0
Citation