FRED Fast Rigid Exhaustive Docking

Previous: 5.7 Complete list of Up: FRED Fast Rigid Exhaustive Next: 6.1 Simple command lines

---

 
6. Example Command Lines

This chapter has example command lines for FRED. The purpose is to connect some concepts of docking to specific parameters in FRED. To that end almost all these examples focus on one idea or concept and the associated parameters (although all examples are complete valid command lines for FRED). It is expected that users will often take multiple examples and combine them on their own command line.

• 6.1 Simple command lines
  • 6.1.1 Docking with an existing receptor
    • 6.1.1.1 Command Line
    • 6.1.1.2 Description
    • 6.1.1.3 Parameters
    • 6.1.1.4 Output Files
  • 6.1.2 Creating a receptor and docking
    • 6.1.2.1 Command Line
    • 6.1.2.2 Description
    • 6.1.2.3 Parameters
    • 6.1.2.4 Output Files
  • 6.1.3 Changing the output file format
    • 6.1.3.1 Command Line
    • 6.1.3.2 Description
    • 6.1.3.3 Parameters
    • 6.1.3.4 Output Files
  • 6.1.4 Setting a prefix and/or an output directory
    • 6.1.4.1 Command Line
    • 6.1.4.2 Description
    • 6.1.4.3 Parameters
    • 6.1.4.4 Output Files
• 6.2 Creating a receptor
  • 6.2.1 With a box
    • 6.2.1.1 Command Line
    • 6.2.1.2 Description
    • 6.2.1.3 Parameters
    • 6.2.1.4 Output
  • 6.2.2 With a bound ligand
    • 6.2.2.1 Command Line
    • 6.2.2.2 Description
    • 6.2.2.3 Parameters
    • 6.2.2.4 Output
  • 6.2.3 With a box and a bound ligand
    • 6.2.3.1 Command Line
    • 6.2.3.2 Description
    • 6.2.3.3 Parameters
    • 6.2.3.4 Output
  • 6.2.4 Without a box or bound ligand
    • 6.2.4.1 Command Line
    • 6.2.4.2 Description
    • 6.2.4.3 Parameters
    • 6.2.4.4 Output
• 6.3 Finding the right pose
  • 6.3.1 Rescoring - scoring without docking
    • 6.3.1.1 Command Line
    • 6.3.1.2 Description
    • 6.3.1.3 Parameters
    • 6.3.1.4 Output
  • 6.3.2 Setting the exhaustive scoring and optimization functions
    • 6.3.2.1 Command Line
    • 6.3.2.2 Description
    • 6.3.2.3 Parameters
    • 6.3.2.4 Output
  • 6.3.3 Adjusting consensus structure - changing weights
    • 6.3.3.1 Command Line
    • 6.3.3.2 Description
    • 6.3.3.3 Parameters
    • 6.3.3.4 Output
  • 6.3.4 Turning consensus structure off
    • 6.3.4.1 Command Line
    • 6.3.4.2 Description
    • 6.3.4.3 Parameters
    • 6.3.4.4 Output
• 6.4 Scoring
  • 6.4.1 One scoring function
    • 6.4.1.1 Command Line
    • 6.4.1.2 Description
    • 6.4.1.3 Parameters
    • 6.4.1.4 Output
  • 6.4.2 Multiple scoring functions
    • 6.4.2.1 Command Line
    • 6.4.2.2 Description
    • 6.4.2.3 Parameters
    • 6.4.2.4 Output
• 6.5 Using MASC
  • 6.5.1 Scoring with MASC
    • 6.5.1.1 Using a single MASC scoring function
    • 6.5.1.2 Description
    • 6.5.1.3 Parameters
    • 6.5.1.4 Output
  • 6.5.2 Using multiple MASC and other scoring functions
    • 6.5.2.1 Command Line
    • 6.5.2.2 Description
    • 6.5.2.3 Parameters
    • 6.5.2.4 Output
  • 6.5.3 Preparing ligands
    • 6.5.3.1 Command Line
    • 6.5.3.2 Description
    • 6.5.3.3 Parameters
    • 6.5.3.4 Output
  • 6.5.4 Preparing ligands with your own reference sites
  • 6.5.5 Preparing ligands
    • 6.5.5.1 Command Line
    • 6.5.5.2 Description
    • 6.5.5.3 Parameters
    • 6.5.5.4 Output
• 6.6 Ligand+Structure based design
  • 6.6.1 Scoring with ligand based design
    • 6.6.1.1 Command Line
    • 6.6.1.2 Description
    • 6.6.1.3 Parameters
    • 6.6.1.4 Output
  • 6.6.2 Docking and scoring with ligand based design
    • 6.6.2.1 Command Line
    • 6.6.2.2 Description
    • 6.6.2.3 Parameters
    • 6.6.2.4 Output

---

				FRED Fast Rigid Exhaustive Docking

Previous: 5.7 Complete list of Up: FRED Fast Rigid Exhaustive Next: 6.1 Simple command lines

---

Documentation released on 7 April 2009.