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« LigandScout Overview
Inte:Ligand: Your partner for in-silico drug discovery
Inte:Ligand illustration
Start Science & Technology Products & Services Company Career Contact
« LigandScout 3.1 Overview
1. Help Overview
2. Introduction to LigandScout
2.1 What's New in LigandScout 3?
2.2 Installing and Starting LigandScout
2.3 Visual Semantics
2.4 LigandScout Graphical User Interface
3. File Handling, Data Management and Networking
3.1 Importing and Exporting Files
3.2 Retrieving PDB Complexes Online
3.3 Local and Shared Repository
3.4 Sessions
3.5 Networking
4. LigandScout Perspectives
4.1 Basic User Interface Modules
4.2 Structure-Based Modeling Perspective
4.3 Ligand-Based Modeling Perspective
4.4 Alignment Perspective
4.5 Screening Perspective
5. Introduction to Pharmacophore Modeling
5.1 Pharmacophore Modeling
5.2 Pharmacophore Feature Definitions
5.3 Editing a Pharmacophore Model
6. Structure-Based Pharmacophore Design
6.1 Structure-Based Pharmacophores
6.2 Creating Structure-Based Pharmacophores
7. Pharmacophore Alignment
7.1 Aligning Pharmacophores and Molecules
7.2 Shared Feature Pharmacophore
7.3 Merged Feature Pharmacophore
8. Ligand-Based Pharmacophore Design
8.1 Ligand-Based Pharmacophores
8.2 Creating Ligand-Based Pharmacophores
9. Virtual Screening
9.1 Virtual Screening in LigandScout
9.2 Preparing a Pharmacophore for Virtual Screening with External Applications
10. LigandScout Settings: Preferences
10.1 Structure-Based Modeling Settings
10.2 Ligand-Based Modeling Settings
10.3 Chemistry Settings
10.4 Library Screening Settings
10.5 Alignment Settings
10.6 Rendering Settings
10.7 Program and Network Settings
A. Appendix
A.1 LigandScout Menu Reference
A.2 LigandScout Icons Reference
A.3 LigandScout Keyboard Shortcuts
A.4 LigandScout Mouse Bindings
A.5 Network Administrator Guide
A.6 Command Line Usage
A.7 Scoring Function
A.8 Calculation of MMFF94 Binding Enthalpies
A.9 Primary Literature
Index

Table of Contents

1. Help Overview
2. Introduction to LigandScout
What's New in LigandScout 3?
Installing and Starting LigandScout
Visual Semantics
LigandScout Graphical User Interface
3. File Handling, Data Management and Networking
Importing and Exporting Files
Retrieving PDB Complexes Online
Local and Shared Repository
Sessions
Networking
4. LigandScout Perspectives
Basic User Interface Modules
Structure-Based Modeling Perspective
Ligand-Based Modeling Perspective
Alignment Perspective
Screening Perspective
5. Introduction to Pharmacophore Modeling
Pharmacophore Modeling
Pharmacophore Feature Definitions
Editing a Pharmacophore Model
6. Structure-Based Pharmacophore Design
Structure-Based Pharmacophores
Creating Structure-Based Pharmacophores
7. Pharmacophore Alignment
Aligning Pharmacophores and Molecules
Shared Feature Pharmacophore
Merged Feature Pharmacophore
8. Ligand-Based Pharmacophore Design
Ligand-Based Pharmacophores
Creating Ligand-Based Pharmacophores
9. Virtual Screening
Virtual Screening in LigandScout
Preparing a Pharmacophore for Virtual Screening with External Applications
10. LigandScout Settings: Preferences
Structure-Based Modeling Settings
Ligand-Based Modeling Settings
Chemistry Settings
Library Screening Settings
Alignment Settings
Rendering Settings
Program and Network Settings
A. Appendix
LigandScout Menu Reference
LigandScout Icons Reference
LigandScout Keyboard Shortcuts
LigandScout Mouse Bindings
Network Administrator Guide
Command Line Usage
Scoring Function
Calculation of MMFF94 Binding Enthalpies
Primary Literature
Index

Contact · Disclaimer

Page designed & authored by G. Wolber
Inte:Ligand: Your partner for in-silico drug discovery
Inte:Ligand illustration
Start Science & Technology Products & Services Company News Career Contact
« LigandScout 3.1 Overview
1. Help Overview
2. Introduction to LigandScout
2.1 What's New in LigandScout 3?
2.2 Installing and Starting LigandScout
2.3 Visual Semantics
2.4 LigandScout Graphical User Interface
3. File Handling, Data Management and Networking
3.1 Importing and Exporting Files
3.2 Retrieving PDB Complexes Online
3.3 Local and Shared Repository
3.4 Sessions
3.5 Networking
4. LigandScout Perspectives
4.1 Basic User Interface Modules
4.2 Structure-Based Modeling Perspective
4.3 Ligand-Based Modeling Perspective
4.4 Alignment Perspective
4.5 Screening Perspective
5. Introduction to Pharmacophore Modeling
5.1 Pharmacophore Modeling
5.2 Pharmacophore Feature Definitions
5.3 Editing a Pharmacophore Model
6. Structure-Based Pharmacophore Design
6.1 Structure-Based Pharmacophores
6.2 Creating Structure-Based Pharmacophores
7. Pharmacophore Alignment
7.1 Aligning Pharmacophores and Molecules
7.2 Shared Feature Pharmacophore
7.3 Merged Feature Pharmacophore
8. Ligand-Based Pharmacophore Design
8.1 Ligand-Based Pharmacophores
8.2 Creating Ligand-Based Pharmacophores
9. Virtual Screening
9.1 Virtual Screening in LigandScout
9.2 Preparing a Pharmacophore for Virtual Screening with External Applications
10. LigandScout Settings: Preferences
10.1 Structure-Based Modeling Settings
10.2 Ligand-Based Modeling Settings
10.3 Chemistry Settings
10.4 Library Screening Settings
10.5 Alignment Settings
10.6 Rendering Settings
10.7 Program and Network Settings
A. Appendix
A.1 LigandScout Menu Reference
A.2 LigandScout Icons Reference
A.3 LigandScout Keyboard Shortcuts
A.4 LigandScout Mouse Bindings
A.5 Network Administrator Guide
A.6 Command Line Usage
A.7 Scoring Function
A.8 Calculation of MMFF94 Binding Enthalpies
A.9 Primary Literature
Index

Library Screening Settings

Library screening settings
Figure 10.14. Library screening settings

Screening Settings Effect
Scoring function Choose the scoring function type that validates the alignments. The Pharmacophore-Fit scoring function only considers pharmacophoric features and the feature RMSD. The Relative Pharmacophore-Fit scores the number of matching pharmacophore features and the RMSD of the pharmacophore alignment normalized to [0..1]. (default: Pharmacophore-Fit)
Screening mode In Match all query features mode the database is browsed to find molecules that are fully matching the given set of query pharmacophores. Whereas in Fragment screening mode, the database molecules are fitted into the query pharmacophores. In the latter case, the query is partially matched. (default: Match all query features)
Retrieval mode Stopping criteria per compound. Stop after first matching conformation: the screening for a molecule stops when the first matched conformation is found. Get best matching conformation: all conformations are examined for the best matching conformation. Get all matching conformation: all conformations that match the query pharmacophore are shown as screening hits. The last two modes could slow down screening. (default: Stop after first matching conformation)
Max. num. of omitted features Defines the maximum number of query features that can be omitted during the Match all query features mode. If zero is specified, the whole query pharmacophore must be matched to be a valid hit. (default: 0)
Min. num. of required features Specifies the minimum number of required features that has to match between the library molecule and the query pharmacophore to be a valid hit. This setting is only enabled if the Fragment screening mode is chosen. (default: 3)
Compound time-out (in minutes) Enables the maximum screening time to spend per compound. (default: off)
Check exclusion volumes Enables the consideration of exclusion volumes during the screening process. (default: enabled)
Enable popup of screening settings dialog Enables the settings dialog of the screening process. (default: enabled)
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Chemistry Settings  Home  Alignment Settings

Contact · Disclaimer

Page designed & authored by G. Wolber

Contact · Disclaimer

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