Table Of Contents - Valdes-Tresanco-MS/AMDock-win GitHub Wiki
- INTRODUCTION
1.1 How to cite AMDock? - DOWNLOAD AND INSTALLATION
- 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 - 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 - APPENDIX
5.1 Change Box specifications on AMDock PyMol plugin
5.2 Making a high-quality image for publications
5.3 Analysing stored results