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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

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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

Rendering Settings

The Renderer Settings allow users to predefine default render styles for the 3D Viewer.

3D General Settings

Figure 10.16. 3D general settings

Default Settings	Effect
Show reference points	Toggles on/off the default visibility of the reference points in the Alignment Perspective. If a pharmacophore or molecule is shown for the first time then the visibility of reference points is assigned according to this flag. (default: disabled)
Show exclusion volumes	Toggles on/off the default visibility of the exclusion volumes in all perspectives except the Structure-Based Modeling Perspective and Bookmark View. If a pharmacophore is shown for the first time then the visibility of exclusion volumes is assigned according to this flag. (default: disabled)
Show co-factors and water	Enables/disables the default visibility of co-factors and water in the Macromolecule View. (default: disabled)
Show active site boxes on mouse-over	Enables/disables the Active Site boxes while moving the mouse over a ligand in the Macromolecule View. (default: disabled)
Simple rendering while moving	If turned on the render style is temporarily switched to line rendering while user interaction (i.e. rotating or translating the visible structure). This feature is especially designed for slower graphics hardware. (default: disabled)
Lock colors of hetero atoms	If enabled, the original colors of hetero atoms remain and cannot be changed. (default: enabled)

Alignment Perspective

Effect

Use blur for focus and context

The check box use Blur toggles between blurring and desaturated coloring of ligands and pharmacophores. (default: disabled)

center added elements

The check box Center Elements toggles centering of the ligand or of the pharmacophore while adding to the Alignment Panel. If enabled, the original coordinates are destroyed and the molecule or pharmacophore is centered in the origin of the model coordinate frame. This behavior can be undesirable if already aligned elements are added from the Alignment Perspective to another view. If you intend to add these elements back, e.g. to the binding pocket, the original coordinates should be retained and this feature should be turned off. (default: disabled)

Surface rendering	Effect
Backface culling	Enables/Disables the backface culling. If enabled all parts of a surface not facing the viewer will not be rendered. (default: disabled)
Front clipping	Enables/Disables the front clipping. If enabled then the surface area closest to the point of view is not rendered. (default: disabled)

General	Effect
Projection	Switch between parallel and perspective projection. (default: perspective)
Projection angle	Switch between normal and wide angle projection. The latter one enhances perspective distortion. (default: normal)
Background color	Switch between black and white background color scheme. (default: black)

3D Renderer Style

Figure 10.17. Renderer style

Default Rendering Styles	Effect
Macromolecule View	Defines the default render styles for macromolecule and ligand in the Macromolecule View . (default: macromolecule: ribbon; ligand: stick)
Active Site View	Defines the default render styles for macromolecule and ligand in the Active Site View . (default: macromolecule: snake; ligand: stick)
Alignment Perspective	Defines the default render styles for ligands and pharmacophores in the Alignment Perspective . (default: stick)

Rendering Settings	Effect
Ball size scaling	Defines a scaling factor which is applied to the ball size representing atoms. (default: 0.200)
Stick size scaling	Defines a scaling factor which is applied to the stick size representing bonds. Depending on this factor the "aromatic ring" thickness is adjusted too. (default: 0.600)

Surface Rendering Settings	Effect
Surface transparency	Changes the surface transparency from being fully translucent (0.0) to opaque (1.0) if alpha blending is enabled in the Render Control menu (default: 0.400). If a surface is currently displayed and Dynamically Update Surface is turned on (menu item in Render Control ) then the transparency setting immediately takes effect. Otherwise, it needs to be updated manually.
Surface extent	This function is only referred to the receptor binding pocket option. The radius of every core atom is calculated whereas the nearest environment atom according to a core atom is taken into account. From that point on, the extent value determines the region (band with) of environment atoms that are included in the calculation of the surface. (default: 2.000 Å)
Surface cutoff	Defines the distance of every core atom to neighboring environment atoms where the surface is cropped. A value of zero means that the surface is cut by the first environment atom. Rising up this value determines the distance from that point. The surface cutoff is only used for receptor binding pockets. (default: 1.000 Å)

2D Depiction

The 2D Depiction Settings allow one to adjust parameters for the 2D depiction of ligand structures.

Figure 10.18. 2D depiction

General	Effect
Time limit for 2D calculation	Defines the maximum calculation time for 2D structures. 2D structure calculation will stop at this limit even if no structure could be retrieved yet. (default: 15.00 sec)

Rendering Options	Effect
Show hydrogens	Specifies which hydrogens should be shown in the 2D depiction. This can be either no hydrogens at all, hydrogens at hetero atoms only, or all hydrogens. (default: show hydrogens for hetero atoms only)
Features	Toggles compact display of hydrogens. If selected the hydrogens to be shown will be drawn as a label. Otherwise, hydrogens will be drawn with a bond to their neighbor atoms. (default: enabled)

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Alignment Settings	Home	Program and Network Settings

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Page designed & authored by G. Wolber

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