Methodology

10. Getting Started...

11. Setting Up AutoGrid and AutoDock Jobs

12. Preparing the Ligand

13. Ligand Flexibility and Constraints

14. Using AutoTors to Define Torsions in the Ligand

15. Running AutoTors

16. Adding Polar Hydrogens to the Macromolecule

17. Running AutoGrid

18. Flexible Docking with AutoDock

19. Monte Carlo Simulated Annealing

20. Genetic Algorithm and Evolutionary Programming Docking

21. Running AutoDock

22. Using the Command Mode in AutoDock

23. Trajectory Files

24. Evaluating the Results of a Docking

25. Visualizing Grid Maps

26. Visualizing Trajectories

Shell Scripts and Awk Programs

Parameters from AutoDock Version 1

AutoDock File Formats

Example Parameter Files

AutoDock References