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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 10. LigandScout Settings: Preferences

Table of Contents

Structure-Based Modeling Settings
PDB Interpretation
Distance Ranges
Hydrogen Bonding
Metal Binding
Hydrophobicity
Aromatic Interactions
Ligand-Based Modeling Settings
Settings and Scoring
Conformer Generation
Clustering
Chemistry Settings
Tautomerization
Tautomer Filters
Force Field: MMFF94
Force Field: Minimization
Library Screening Settings
Alignment Settings
Alignment
Rendering Settings
3D General Settings
3D Renderer Style
2D Depiction
Program and Network Settings
Main Settings
PDB and Proxy
Distributed Calculation
LigandScout supports a plenitude of customizable settings. The Preferences can be accessed from the Edit menu on Linux and Windows systems, and from the LigandScout menu on Mac OSX platforms, respectively. This panel is composed of eight major settings areas:
  1. Structure-Based Modeling Settings
  2. Ligand-Based Modeling Settings
  3. Chemistry Settings
  4. Library Screening Settings
  5. Alignment Settings
  6. Rendering 3D and 2D Settings
  7. Program and Network Settings
Every entry of the Preferences dialog exhibits a Default button and All Default button. The Default button sets the current preference tab to their default settings (e.g. PDB interpretation tab). All Defaults sets the whole Preferences dialog to factory defaults.
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Page designed & authored by G. Wolber