FRED Fast Rigid Exhaustive Docking

Previous: 4.4 Output Up: FRED Fast Rigid Exhaustive Next: 5.1 Specifying Parameters

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5. Running FRED

• 5.1 Specifying Parameters
• 5.2 Command Line Help
• 5.3 Receptor file
  • 5.3.1 File Format
  • 5.3.2 Querying
    • 5.3.2.1 Reasonable contour values
    • 5.3.2.2 Example
  • 5.3.3 GUI Creation
  • 5.3.4 Command Line Creation
    • 5.3.4.1 Preparing the protein
• 5.4 Constraints
  • 5.4.1 Protein constraints
  • 5.4.2 Custom constraints
    • 5.4.2.1 Basic constraint file
    • 5.4.2.2 Constraints with multiple spheres
    • 5.4.2.3 Multiple constraints
    • 5.4.2.4 Constraints with SMARTS
    • 5.4.2.5 Complex example
    • 5.4.2.6 Centering spheres on atoms
• 5.5 Preparing ligand database
  • 5.5.1 Protonation state
  • 5.5.2 Charging molecules
  • 5.5.3 Generating conformers
• 5.6 Screen output
• 5.7 Complete list of output files
  • 5.7.1 Setup File
  • 5.7.2 Status File
  • 5.7.3 Information message log
  • 5.7.4 Warning log
  • 5.7.5 Receptor file
  • 5.7.6 Score Files
  • 5.7.7 Docked Structure Files
  • 5.7.8 Alternate Score Files
  • 5.7.9 Alternate Docked Structure Files
  • 5.7.10 Consensus Hitlist
  • 5.7.11 MASC Consensus Hitlists
  • 5.7.12 Undocked Ligand Files

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				FRED Fast Rigid Exhaustive Docking

Previous: 4.4 Output Up: FRED Fast Rigid Exhaustive Next: 5.1 Specifying Parameters

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Documentation released on August 12, 2008.