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Valdes-Tresanco-MS / AMDock-win Public

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MARIO edited this page Oct 7, 2020 · 4 revisions

Toggle table of contents Pages 24

Home
1. INTRODUCTION
1.1 Cite AMDock
2. DOWNLOAD AND INSTALLATION
3. AMDock WORKFLOW and GUI
4. TUTORIALS
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
Table Of Contents

TABLE OF CONTENTS

INTRODUCTION

CITE AMDOCK

INSTALLATION

WORKFLOW and GUI

Simple Docking
Off-target Docking
Scoring
Additional tutorials

Box customization
High Quality Images
Analyze stored results

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