Contents

• Automated Docking 5
• Introduction 5
• Overview of the Method 6
• Applications 7
• What's New 9
• Theory 11
• Overview of the Free Energy Function 11
• Grid Maps 13
• Van der Waals Potential Energy 15
• Modelling Hydrogen Bonds 20
• A note on atom type codes: 21
• Electrostatic Potential Grid Maps 22
• Methodology 24
• Getting Started... 24
• Setting Up AutoGrid and AutoDock Jobs 25
• Preparing the Ligand 26
• Ligand Flexibility and Constraints 26
• Using AutoTors to Define Torsions in the Ligand 28
• Ligand is in PDBQ-format: 28
• Ligand is in Mol2-format: 28
• AutoTors Output: 28
• AutoTors Flags: 29
• Running AutoTors 30
• Input Stage 31
• Root Specification Stage 31
• Torsions Detection and Selection Stage 31
• Root Expansion and Output Stage 32
• Adding Polar Hydrogens to the Macromolecule 32
• Running AutoGrid 33
• Flexible Docking with AutoDock 33
• Monte Carlo Simulated Annealing 35
• Genetic Algorithm and Evolutionary Programming Docking 36
• Running AutoDock 37
• Using the Command Mode in AutoDock 38
• Trajectory Files 41
• Evaluating the Results of a Docking 42
• Visualizing Grid Maps 43
• Visualizing Trajectories 43
• Shell Scripts and Awk Programs 45
• Parameters from AutoDock Version 1 56
• AutoDock File Formats 57
• Protein Data Bank with Partial Charges: PDBQ 57
• PDBQ with Solvation Parameters: PDBQS 57
• AutoGrid Grid Parameter File: GPF 58
• AutoGrid Keywords and Commands 59
• Grid Map File 61
• Grid Map Field File 61
• AutoDock Docking Parameter File: DPF 62
• Command to set the seed for the random number generator 63
• Parameters defining the grid maps to be used 63
• Parameters defining the ligand and its initial state 64
• Parameters defining ligand step sizes 65
• Parameters defining optional ligand torsion constraints 66
• Parameter affecting torsional free energy 67
• Parameters for ligand internal energies 68
• Parameters for simulated annealing searches 68
• Parameter to set the amount of output 70
• Parameters for trajectory output during SA dockings 70
• Parameter for energies of atoms outside the grid 71
• Parameter for initializing the ligand in SA 71
• Parameters for cluster analysis of docked conformations 71
• Parameters for re-clustering the results of several jobs 72
• Parameters for genetic algorithm, Lamarckian GA and evolutionary programming searches 72
• Command to set genetic algorithm parameters 73
• Parameters for local search 74
• Commands to choose and set the local search method 75
• Commands to perform automated docking 75
• Command to perform clustering of docked conformations 76
• Example Parameter Files 77
• AutoGrid GPF 77
• AutoDock DPF 78
• Example 1: Docking using Monte Carlo Simulated Annealing 78
• Example 2: Clustering Many Dockings 79
• Example 3: Docking Using the Lamarckian Genetic Algorithm (LGA) 80
• AutoDock References 82
• Primary References 82
• AutoDock 3.0 82
• AutoDock 2.4 82
• AutoDock 1.0 83
• Reviews of Applications 83
• Selected Applications and Citations of AutoDock 83
• Web publications 85