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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 6. Structure-Based Pharmacophore Design
Table of Contents
Structure-Based Pharmacophores
Why Use Structure-Based Pharmacophores?
Basic Workflow
Creating Structure-Based Pharmacophores
Data Import and Structure Preparation
Automated Generation of Structure-Based Pharmacophores
Creating Advanced Structure-Based Pharmacophore Models
Creating Excluded Volumes Coat
Creating Pharmacophore Models from Injected Ligands
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Disclaimer
Page designed & authored by G. Wolber