Brood: Fragment replacement for Medicinal Chemistry

Previous: Front Matter Up: Brood: Fragment replacement for Next: 1. Introduction

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Contents

• 1. Introduction
• 2. Theory
  • 2.1 Bioisosteric searching
  • 2.2 Classes of Bioisosteres
  • 2.3 Database generation
• 3. Usage
  • 3.1 Command Line Interface
    • 3.1.1 Required Parameters
    • 3.1.2 Molecular File Formats
    • 3.1.3 Optional Parameters
  • 3.2 Example executions
• 4. External Files
  • 4.1 Input Files
    • 4.1.1 Query files
    • 4.1.2 Bioisostere fragment database
    • 4.1.3 Example fragment files
  • 4.2 Output Files
    • 4.2.1 Info File
    • 4.2.2 Param File
    • 4.2.3 Log File
    • 4.2.4 Report File
    • 4.2.5 Hitlist Files
    • 4.2.6 Build Files
• 5. Database Preparation
  • 5.1 Database Fragmentation
    • 5.1.1 Theory
    • 5.1.2 Usage
  • 5.2 Conformers and Charges
• A. Release Notes
  • A.1 Brood 1.1
  • A.2 Brood 1.0
• Bibliography

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				Brood: Fragment replacement for Medicinal Chemistry

Previous: Front Matter Up: Brood: Fragment replacement for Next: 1. Introduction

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Documentation released on 13 August 2007.