Table Of Contents

1. INTRODUCTION
   1.1 How to cite AMDock?
2. DOWNLOAD AND INSTALLATION
3. AMDock WORKFLOW and GUI
   3.1 Main tab
   3.1.1 Defining a working directory
   3.1.2 Preparing input files
   3.1.3 Defining a search space
   3.1.4 Run docking
   3.1.5 Analysis of results
   3.2 Results Analysis tab
   3.3 Configuration and Info tabs
4. TUTORIALS
   4.1 Before beginning...
   4.2 Simple docking
   4.2.1 “Custom box” with Autodock4Zn
   4.2.2 “Box centered on Hetero” using Autodock Vina
   4.2.2.1 re-Docking experiment
   4.2.2.2 Docking a similar ligand
   4.2.3 “Centered on residue(s)” using AutoDock Vina
   4.2.4 “Automatic” mode using AutoDock Vina
   4.3 Off-target docking
   4.4 Scoring
   4.5 Additional Tutorials
   4.5.1 In unity, strength...
   4.5.2 Docking to allosteric binding sites
   4.5.3 Input a customized AD4 parameter file
5. APPENDIX
   5.1 Change Box specifications on AMDock PyMol plugin
   5.2 Making a high-quality image for publications
   5.3 Analysing stored results