Using AutoDock for Ligand‐Receptor Docking

Garrett M. Morris1, Ruth Huey1, Arthur J. Olson1

1 The Scripps Research Institute, La Jolla, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.14
DOI:  10.1002/0471250953.bi0814s24
Online Posting Date:  December, 2008
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Abstract

This unit describes how to set up and analyze ligand‐protein docking calculations using AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring function is a subset of the AMBER force field that treats molecules using the United Atom model. The unit uses an X‐ray crystal structure of Indinavir bound to HIV‐1 protease taken from the Protein Data Bank (UNIT 1.9) and shows how to prepare the ligand and receptor for AutoGrid, which computes grid maps needed by AutoDock. Indinavir is prepared for AutoDock, adding the polar hydrogens, and partial charges, and defining the rotatable bonds that will be explored during the docking. The input files for AutoGrid and AutoDock are created, and then the grid map calculation run, followed by the docking calculation in AutoDock. Finally, this unit describes some of the ways the results can be analyzed using AutoDockTools. Curr. Protoc. Bioinform. 24:8.14.1‐8.14.40. © 2008 by John Wiley & Sons, Inc.

Keywords: AutoDock; protein‐ligand docking; virtual screening; computer‐aided drug design

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Download and Install AutoDock, AutoGrid, and AutoDockTools
  • Basic Protocol 2: Preparing the Macromolecule
  • Basic Protocol 3: Preparing the Ligand
  • Basic Protocol 4: Saving the Macromolecule in PDBQT Format
  • Basic Protocol 5: Preparing the Flexible Residues (Optional)
  • Basic Protocol 6: Preparing the Grid Parameter File
  • Basic Protocol 7: Starting AutoGrid 4
  • Basic Protocol 8: Setting Up the Docking
  • Basic Protocol 9: Starting AutoDock 4
  • Basic Protocol 10: Reading Docking Logs
  • Basic Protocol 11: Visualizing Docked Conformations
  • Basic Protocol 12: Clustering Conformations
  • Basic Protocol 13: Visualizing Conformations in the Complex
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
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