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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 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

LigandScout Mouse Bindings

All Views and Panels

Mouse Button	Activity	Effect
LEFT	click	Select single element
LEFT	double click	Extend selection to whole element; Macromolecule View : Select whole macromolecule; Active Site View : Select whole ligand, amino acid, or pharmacophore
SHIFT+LEFT	press	2D and 3D View: Box selection Hierarchy View, Select consecutive elements
CTRL+LEFT	click	Expand selection: Select individual elements

3D View

Mouse Button	Activity	Effect
LEFT	press	Rotate
LEFT	click	Select single element
MIDDLE/WHEEL	press or scroll	Zoom in or out
RIGHT	press	Translate

3D Alignment Perspective

For the following interactions it is assumed that at least one element was highlighted (yellow).

Mouse Button	Activity	Effect
ALT+SHIFT+LEFT	press	Rotate, but alter coordinates of the selected elements
ALT+SHIFT+RIGHT	press	Translate, but alter coordinates of the selected elements

Prev	Up	Next
LigandScout Keyboard Shortcuts	Home	Network Administrator Guide

Contact · Disclaimer

Page designed & authored by G. Wolber

Contact · Disclaimer