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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
Appendix A. Appendix
Table of Contents
LigandScout Menu Reference
File
Edit
Library
Ligand-Set
Molecule
Pharmacophore
Align & Merge
Render Control
Surface
Window
Help
LigandScout Icons Reference
Toolbar
Hierarchy View
Copyboard Widget
Alignment Panel
Bookmarks Panel
Library View
Library: Alternatives Switcher
Ligand-Based Modeling Perspective Toolbar
Screening Toolbar
Preferences Settings
LigandScout Keyboard Shortcuts
LigandScout Mouse Bindings
All Views and Panels
3D View
3D Alignment Perspective
Network Administrator Guide
Discovery of iworkers and Connection Establishment
Communication Protocol
Failure Tolerance/Error Treatment
Summary of Network Information
Command Line Usage
Conformation Generation
Ligand-based Pharmacophore Generation
Virtual Screening
Networking: iworker
Retrieving Library Size
Retrieving Database Information
Merging Databases
Retrieving Start Position File from Library
Retrieving System ID
LigandScout License Activation
Scoring Function
Simple Geometric Scoring Function (“
Pharmacophore-Fit
”)
Atom Sphere Overlap (“
Fast Shape
”)
Gaussian Shape Similarity
Pharmacophore-Fit and Atom Overlap
Calculation of MMFF94 Binding Enthalpies
Primary Literature
Primary reference describing methods and algorithms
More information on pharmacophoric alignment algorithm
Applications
Short Surveys
Talks
Contact
·
Disclaimer
Page designed & authored by G. Wolber