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« 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
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Page designed & authored by G. Wolber

Inte:Ligand: Your partner for in-silico drug discovery

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

Alignment Settings

The Alignment Settings allow customizations for the alignment of arbitrary combinations of molecules and/or pharmacophores. These settings are applied, depending on the active scheme.

Alignment

Figure 10.15. Alignment settings

Alignment	Effect
Active scheme	Specifies the settings scheme for alignments in the screening process (Match all query, Fragment screening), ligand-based model creation or Alignment Perspective.
Maximum stored alignments	Defines the maximum number of stored alignments. In case there will be more alignments during the execution of the alignment algorithm, only the best will be kept and the others will be discarded. Note: The so called Pharmacophore-Fit scoring function (considers number of features and RMS) is used. The scoring function can be customized only in the ligand-based settings to generate ligand-based pharmacophores. (default for Alignment Perspective and ligand-based model creation: 20; Screening: 1 )
Discard alignments threshold	Defines the maximum allowed RMS (root mean squared) deviation of structures to be considered alignable. Alignments exceeding this limit are rejected. The RMS calculation is based on valid matched feature pairs of both structures. (default: 3.00 RMS)
Similarity threshold	For every generated alignment a rotation is stored. Depending on the deviation of the three unit vectors under this mapping an alignment will be discarded if it is too similar to a previous one. Certainly, it will be checked which alignment has the better RMS value and this one will be kept. (default: 5.0)
Omitted features in similarity matrix	Defines how many features can be omitted during alignment. Alignments will be generated by combinatorially excluding the specified number of features. This means that the more features are left out, the longer the generation process will take (NOTE: exponential growth). (default: 1)
Plane feature deviation	Defines the maximum deviation of the normal vectors of two plane features to be included in an alignment. If the angle between the normal vectors exceeds the specified value, there will be no valid match between these two plane features. (default: 25°)

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Page designed & authored by G. Wolber

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