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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
Chapter 5. Introduction to Pharmacophore Modeling
Table of Contents
Pharmacophore Modeling
Pharmacophore Definition
Pharmacophore Feature Definitions
Pharmacophore Feature Constraint Types
Pharmacophore Feature Definitions
Editing a Pharmacophore Model
Create New Features and Change Feature Types
Deleting Selected Features
Deleting All Features at Once
Increasing/Decreasing the Tolerance of Selected Features
Edit Feature Weight
Marking Features
This chapter provides general information about pharmacophore concepts.
Pharmacophore Modeling
Pharmacophore Feature Definitions
Editing a Pharmacophore Model
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Page designed & authored by G. Wolber