• OEApplications 2025.2
    • Highlights of Applications Release 2025.2
      • Shape: Features Extension
      • Saiph TK: New Toolkit for ETL
      • OEChem TK and Spruce TK: Improvements to CIF File Format Support
      • Supported Platforms
      • Related Application Versions
    • Detailed Release Notes 2025.2
      • AFITT
      • BROOD
        • Related Toolkit Information
      • EON
        • Related Toolkit Information
      • OEDOCKING
        • Related Toolkit Information
      • OMEGA
        • Related Toolkit Information
      • PICTO
        • Related Toolkit Information
      • PKA-PROSPECTOR
      • QUACPAC
        • Related Toolkit Information
      • ROCS
        • New Features
        • Related Toolkit Information
      • SITEHOPPER
        • Related Toolkit Information
      • SPRUCE
        • New Features
        • Minor Bug Fixes
        • Related Toolkit Information
      • SZMAP
        • Related Toolkit Information
      • SZYBKI
        • Related Toolkit Information
    • Previous Release Highlights
      • Highlights of Applications Release 2025.1
        • FastROCS: Grid Query Support
        • Bioisostere TK: Feature Extensions
        • SZYBKI: Robust Protein–Ligand Optimization
        • Supported Platforms
        • Related Application Versions
      • Release Highlights 2024.2.1
      • Release Highlights 2024.2.0
        • OMEGA: Thompson Sampling for Torsion Driving
        • BROOD: Bioisosteric Fragment Replacement in Macrocyclic Peptides
        • Eon TK: New Toolkit for Overlay Optimization with Shape and Charge Density
      • Supported Platforms
      • Related Application Versions
      • 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
      • 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: Make Receptor (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
  • Applications
    • 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 3.0.3.1
      • 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
        • FLYNN 3.0.3
        • FLYNN 3.0.2
        • AFITT 3.0.1
        • 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 4.2.1.1
      • Introduction
        • Applications
        • Utility Programs
        • Installing the BROOD Database
      • vBROOD
        • Overview
        • Build and Run
        • Build a New Query
        • Run BROOD
        • 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 4.2.1
        • BROOD 4.2.0
        • BROOD 4.1.0
        • Bioisostere TK 4.1.0
        • 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 3.1.2.1
      • Introduction
        • Overview
        • Applications
      • EON
        • Overview
        • Example Commands
        • Report File
        • Command Line Help
        • Required Parameters
        • Optional Parameters
      • Theory
      • Release History
        • EON 3.1.2
        • EON 3.1.1
        • EON 3.1.0
        • Eon TK 3.1.0
        • Zap TK 2.5.0
        • 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 4.3.4.1
      • 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
      • Make Receptor
        • Overview
        • GUI Layout
        • Setting up a Receptor
      • Utilities
        • ReceptorInDU
        • OEB2DUReceptor
        • DockingReport
        • ScorePose
        • ReceptorToolbox
        • combine_receptors
        • DU2OEBReceptor
      • Release History
        • OEDocking 4.3.4
        • OEDocking 4.3.3
        • OEDocking 4.3.2
        • OEDocking TK 4.3.2
        • 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 6.1.1.1
      • 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 6.1.1
        • OMEGA 6.1.0
        • OMEGA 6.0.0
        • Omega TK 6.0.0
        • MolProp TK 2.6.5
        • 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 5.1.4.1
      • Introduction
        • Overview
        • Applications
      • PICTO
        • Overview
        • Sketcher
        • SMARTS
        • Implicit/Explicit Hydrogens
        • Atom Labeling, Aromatic Displays, Aromatic Modeling, and other Displays
      • Release History
        • PICTO 5.1.4
        • PICTO 5.1.3
        • PICTO 5.1.2
        • OEDepict TK 2.5.5
        • 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 1.2.6.1
      • 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 1.2.6
        • pKa-Prospector 1.2.5
        • pKa-Prospector 1.2.4
        • 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 2.2.7.1
      • 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 2.2.7
        • Quacpac 2.2.6
        • QUACPAC 2.2.5
        • Quacpac TK 2.2.5
        • QUACPAC 2.2.4
        • Quacpac TK 2.2.4
        • 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 3.9.0.1
      • 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 3.9.0
        • ROCS 3.8.0
        • ROCS 3.7.0
        • Shape TK 3.7.0
        • 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 2.1.3.1
      • 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 2.1.3
        • SiteHopper 2.1.2
        • SiteHopper 2.1.1
        • SiteHopper TK 2.1.1
        • 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 1.8.0.1
      • 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 1.8.0
        • SPRUCE 1.7.0
        • SPRUCE 1.6.1
        • Spruce TK 1.6.1.1
        • Spruce TK 1.6.1
        • 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 1.7.3.1
      • 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 1.7.3
        • SZMAP 1.7.2
        • SZMAP 1.7.1
        • Szmap TK 1.7.1
        • 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 2.9.1.1
      • 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
        • Nonplanar Aromatic Rings in Protein-Bound Ligands
        • Freeform Theory
      • Utilities
        • OptLigandInDU
        • OptimizeDU
      • Release History
        • SZYBKI 2.9.1
        • SZYBKI 2.9.0
        • SZYBKI 2.8.0
        • Szybki TK 2.8.0
        • 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 5.0.7.2
      • 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 5.0.7
        • 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 »
  • Contents »
  • Applications »
  • pKa-Prospector 1.2.6.1

pKa-Prospector 1.2.6.1

  • Introduction
    • Overview
    • Applications
  • pKa-Prospector
    • Overview
    • QuickStart
      • Open a molecule
      • Edit the Molecule
      • Perform a Substructure Search
      • Open up a Result Report
      • Save it to PDF
    • Query Molecule
      • Tautomers
    • Property Filters
      • pKa and Temperature
      • Ionization Types
      • Quality Minimum
    • Search Buttons
      • Analog Search
      • Exact Search
      • Property Search
      • Substructure Search
      • Similarity Search
    • Results View
      • Search Summary
      • Depiction
      • Results Table
    • Preferences
      • Results View Customization
      • Search Options
    • Result Report
      • Depiction
      • Summary
      • Full Listing
      • Saving
    • Menu Items
      • Saving Data
      • Session History
      • Query Bookmarks
    • Appending Data
      • Data Formatting
      • Data Mapping
      • Extra Data
    • Selecting an Imported Database
      • Select Database
  • Release History
    • pKa-Prospector 1.2.6
    • pKa-Prospector 1.2.5
    • pKa-Prospector 1.2.4
    • pKa-Prospector 1.2.3
    • pKa-Prospector 1.2.2
    • pKa-Prospector 1.2.1
      • Minor bug fixes
    • pKa-Prospector 1.2.0
    • pKa-Prospector 1.1.7
    • pKa-Prospector 1.1.6
      • Fall 2021
    • pKa-Prospector 1.1.5
      • July 2021
    • 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
      • Minor bug fixes
    • pKa-Prospector 1.0.0
      • Features
  • Citation
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