Methodology

11. Getting Started...

9. Setting Up AutoGrid and AutoDock Jobs

10. Preparing the Ligand

11. Ligand Flexibility and Constraints

12. Using AutoTors to Define Torsions in the Ligand

13. Running AutoTors

14. Adding Polar Hydrogens to the Macromolecule

15. Running AutoGrid

16. Flexible Docking with AutoDock

17. Monte Carlo Simulated Annealing

18. Genetic Algorithm and Evolutionary Programming Docking

19. Running AutoDock

20. Using the Command Mode in AutoDock

21. Trajectory Files

22. Evaluating the Results of a Docking

23. Visualizing Grid Maps

24. Visualizing Trajectories

Shell Scripts and Awk Programs

Parameters from AutoDock Version 1





AutoDock File Formats

Example Parameter Files

AutoDock References