Graphical Interface¶
Overview¶
BROOD includes a graphical interface that gives access to all the command-line features as well as some features, such as query editing and placing contraint atoms, that are very difficult to utilize from the command-line alone.
Welcome Screen¶
Task Menu¶
Edit Menu¶
Preference Menu¶
File Menu¶
Query Editing¶
Build a Query Task¶
Load a Molecule¶
Load a Protein¶
Property Examination¶
Fragment Selection¶
Color Force-Field¶
Attachment Points¶
Query Editing Tools¶
Color-Atom Tool¶
Color-Constraint Tool¶
Adding Constraints¶
Custom-Constraints¶
Substructure Editor¶
Substructure Browser¶
Custom Substructure Selection¶
Custom-Constraint Table¶
Protein Visibility¶
Running a BROOD Search¶
Run Brood Task¶
Loading Queries From Session¶
Loading Recent Queries¶
Loading Saved Queries¶
Query Details Reporting¶
Adding a Protein to a Query¶
Protein Visibility¶
Optional Property Filtering¶
Loading Recent Filters¶
Loading Saved Filters¶
Filter Property Quick-View¶
BROOD Search Parameters¶
Advanced Parameter Access¶
Output Prefix¶
Quick Search¶
Require Rings¶
Search Type¶
Output Directory¶
CSV File Creation¶
Run BROOD Search¶
Advanced: Database¶
Advanced: Database Navigation¶
Advanced: Dots¶
Advanced: MPI¶
Advanced: Other¶
Advanced: Hitlist Size¶
Advanced: Update Frequency¶
Advanced: Output Format¶
Advanced: Other Output¶
While the Search Runs¶
Intermediate Results¶
Opening the New Hitlist¶
Results Depictions¶
Results Output¶
Results Status¶
Property Profile Design¶
Property Filter Task¶
Database and Hitlist Filtering¶
Reference Query¶
Recent Reference Queries¶
Default Filters¶
Property Histograms¶
Drag and Drop Filtering¶
Value-based Filtering¶
Reading the Histograms¶
Filter Interdependence¶
Boolean Filters¶
Saving a Database Filter¶
Database Filter Dialog¶
Saving a Filtered Hitlist¶
Filtered Hitlist Dialog¶
Viewing Saved Results¶
Quick visual inspection of preliminary Brood results can take place inside the lead-optimization visual interface. Thorough visual inspection of complete Brood results is designed to take place inside VIDA. Brood comes with a VIDA extension that facilitates exploration of the Brood results.
View Results Task¶
Loading Recent Results¶
Loading Saved Results¶
Viewing Multiple Results¶
Results Hierarchy Browser¶
Results Viewer Introduction¶
Results Viewer Control Panel¶
Query and Cluster-Heads¶
Molecular Navigation¶
Left-Right Cluster Navigation¶
Query-Ligand Overlay¶
Query Display¶
The Active Ligand (Blue Box)¶
Protein Display¶
Hydrogen-Bonds¶
Multi-Structure View¶
Number of Structures¶
2D/3D View¶
Property View¶
Property Detachment¶
Activity Belief Model¶
Calculated Properties¶
Cluster Drill-Down¶
Cluster View and Navigation¶
Adding Favorites¶
Viewing Favorties¶
Removing Favorites¶
Saving Favorties¶
Deleting Molecules¶
Recovering Deleted Molecules¶
HotKeys¶
Protein Surface Display¶
Table Of Contents
- Graphical Interface
- Overview
- Query Editing
- Build a Query Task
- Load a Molecule
- Load a Protein
- Property Examination
- Fragment Selection
- Color Force-Field
- Attachment Points
- Query Editing Tools
- Color-Atom Tool
- Color-Constraint Tool
- Adding Constraints
- Custom-Constraints
- Substructure Editor
- Substructure Browser
- Custom Substructure Selection
- Custom-Constraint Table
- Protein Visibility
- Running a BROOD Search
- Run Brood Task
- Loading Queries From Session
- Loading Recent Queries
- Loading Saved Queries
- Query Details Reporting
- Adding a Protein to a Query
- Protein Visibility
- Optional Property Filtering
- Loading Recent Filters
- Loading Saved Filters
- Filter Property Quick-View
- BROOD Search Parameters
- Advanced Parameter Access
- Output Prefix
- Quick Search
- Require Rings
- Search Type
- Output Directory
- CSV File Creation
- Run BROOD Search
- Advanced: Database
- Advanced: Database Navigation
- Advanced: Dots
- Advanced: MPI
- Advanced: Other
- Advanced: Hitlist Size
- Advanced: Update Frequency
- Advanced: Output Format
- Advanced: Other Output
- While the Search Runs
- Intermediate Results
- Opening the New Hitlist
- Results Depictions
- Results Output
- Results Status
- Property Profile Design
- Property Filter Task
- Database and Hitlist Filtering
- Reference Query
- Recent Reference Queries
- Default Filters
- Property Histograms
- Drag and Drop Filtering
- Value-based Filtering
- Reading the Histograms
- Filter Interdependence
- Boolean Filters
- Saving a Database Filter
- Database Filter Dialog
- Saving a Filtered Hitlist
- Filtered Hitlist Dialog
- Viewing Saved Results
- Results Hierarchy Browser
- Results Viewer Introduction
- Results Viewer Control Panel
- Query and Cluster-Heads
- Molecular Navigation
- Left-Right Cluster Navigation
- Query-Ligand Overlay
- Query Display
- The Active Ligand (Blue Box)
- Protein Display
- Hydrogen-Bonds
- Multi-Structure View
- Number of Structures
- 2D/3D View
- Property View
- Property Detachment
- Activity Belief Model
- Calculated Properties
- Cluster Drill-Down
- Cluster View and Navigation
- Adding Favorites
- Viewing Favorties
- Removing Favorites
- Saving Favorties
- Deleting Molecules
- Recovering Deleted Molecules
- HotKeys
- Protein Surface Display
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Installation and Platform Notes