BROOD 4.0.0.0

• Introduction
  • Applications
  • Utility Programs
  • Installing the BROOD Database
• vBROOD
  • Overview
  • Build and Run
    • Build a New Query
    • Selecting a filter
    • Setting up BROOD
    • Run BROOD
  • Build a New Query
    • Loading a molecule
    • Selecting a fragment for replacement
    • Fixing problems
    • Editing fragments
    • Finishing up
  • Run BROOD
    • Loading a query
    • Selecting a filter
    • Setup BROOD
    • Run BROOD
  • Filtering
    • The Filter window
    • Filtering
    • Setting up a filter
  • View Results
  • Viewing Results in VIDA
    • Getting started
    • Viewing Clusters
• BROOD
  • Overview
  • Input Files
    • Query Files
    • Fragment Database
    • Example Fragment Files
    • Molecular File Formats
  • Example Commands
  • Command Line Help
  • Parameters
    • Execution Parameters
    • Input Parameters
    • Output Parameters
    • Control Parameters
    • Advanced Parameters
    • Property selection
    • Synthetic Properties
    • Derived Property Selection
  • Output Files
    • Info File
    • Param File
    • Log File
    • Report File
    • Hitlist File
    • Removed File
• CHOMP
  • Overview
  • Example Commands
  • Command Line Help
  • Required Parameters
  • Optional Parameters
    • Execute Options
• Utilities
  • Overview
  • Command Line Help
  • Example Commands
  • Required Parameters
  • Optional Parameters
• Overview
• Human Complement C3a Receptor Example
  • Specifying the database
  • Loading a molecule
  • Editing the query
  • Selecting properties
    • Using the property filter (optional)
  • Setting up the BROOD search
  • Opening and viewing results
  • Exploring the Results
    • Keyboard shortcuts for navigating BROOD results
    • Brood results in the Results Viewer
    • Working with Favorites in the BROOD Results Viewer
• Fragment Joining Tutorial
  • BROOD database
  • Loading two molecules
  • Loading the protein
  • Choosing a query
  • Setting up a search
  • Examining the Log files
  • Viewing results in a protein site
• Generating a Database with Crystallographic Conformations
  • Preparing data sources
  • Generating a database
  • Advanced topic: editing the fragments at an intermediate step
• Theory
  • Theory
    • Fragment similarity searching
    • Clash detection and selectivity
    • Strain energy
    • Fragment joining
    • Cyclization
    • Molecular complexity
    • Aromatic fragment comparison
    • Shape-based belief model
    • Abbott bioavailability score
    • BROOD Database Generation (CHOMP)
    • BROOD Database
  • Fragment joining
  • Cyclization
  • BROOD Database Generation (CHOMP)
• BROOD Fragment Database
  • ChEMBL31 Fragment Database
  • ChEMBL31_lite Fragment Database
  • brood-database-chembl-3.0.0
• Release History
  • BROOD 4.0.0
    • Major bug fixes
  • Bioisostere TK 4.0.0
    • New features
  • BROOD 3.2.2
    • Minor bug fixes
  • BROOD 3.2.1
    • Minor bug fixes
  • BROOD 3.2.0
    • New Features
    • Major bug fixes
  • BROOD 3.1.7
  • BROOD 3.1.6
  • BROOD 3.1.5
  • BROOD 3.1.4.0
    • Documentation changes
  • BROOD 3.1.3
    • Minor bug fixes
  • BROOD 3.1.2
    • Major bug fixes
    • Minor bug fixes
  • BROOD 3.1.1
    • Major bug fixes
  • BROOD 3.1.0
    • Minor bug fixes
  • BROOD 3.0.0
    • Platform Support
    • vBROOD
    • Results Viewer
    • BROOD
    • CHOMP
    • Merge
  • BROOD 2.0.0
    • New Features:
  • BROOD 1.1.2
  • BROOD 1.1.1
  • BROOD 1.1.0
  • BROOD 1.0.1
  • BROOD 1.0.0
  • BROOD 0.9.b2
  • BROOD 0.9.b1
• Citation