AutoDock4

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AutoDock4


AutoDock is a molecular modeling simulation software. It is specifically used for protein-ligand docking. AutoDock consists of a suite of automated docking tools. They are designed to predict how small molecules, such as substrates or drug candidates bind to a receptor of known 3D structure. In addition to using them for docking, the atomic affinity grids can also be visualized. This can help synthetic organic chemists design better binders. Autodock4 is a computational docking program based on an empirical free energy force field and rapid Lamarckian genetic algorithm search method.

The Spoken Tutorial Effort for AutoDock4 has being contributed by Dr. Snehalatha Kaliappan and Ms. Madhuri Ganapathi with domain reviews done by Ms. Sruthi Sudhakar, Chemistry Dept, IIT Bombay.

Learners: Undergraduate and post-graduate students, research scholars in the fields of Chemistry, Biochemistry, Molecular Biology, Bioinformatics.

Drug-discovery experts, Pharmaceutical company scientists.


Contents

Basic Level

1. Installation of AutoDock4 on Linux OS

  • Visit AutoDock website.
  • Download AutoDock suite 4.2.6 installer file for Linux OS.
  • Visit MGL tools web page.
  • About MGL tools.
  • Download MGL tools 1.5.7 installer file.
  • Download User Manual and Examples PDF file.
  • Installation of AutoDock on Linux 20.04 OS.
  • Installation of MGL tools.
  • Open the README file and check the instructions for creating aliases.
  • Open bashrc file and change the path for the location of mgl tools files.
  • Create aliases for using ADT and PMV.
  • Open the GUI for ADT and PMV.


2. Getting Started with Docking

  • Visit RCSB Protein Data Bank website.
  • Download ligand and protein files from the RCSB database.
  • Move the downloaded files to home folder.
  • Open ADT interface using the terminal.
  • Perform ligand refinement using AutoDockTools.
  • Add hydrogens to the ligand structure.
  • Save the structure as PDB file.
  • Display root atom.
  • Display allowed torsions in the ligand structure
  • Save the refined ligand as pdbqt file.


3. Receptor Preparation for Docking

  • Open the ADT GUI.
  • Open the receptor pdb file on the ADT display panel.
  • Delete the water molecules from the receptor structure.
  • Add hydrogens to the receptor structure.
  • Remove the ligand molecule crystallized along with the receptor.
  • Save the current session.


4. Running AutoGrid

  • Open the saved .psf session file in ADT.
  • Save the receptor file as pdbqt file.
  • About the grid box.
  • Set the grid box parameters.
  • Create a grid for the receptor molecule.
  • Save the grid box properties as .gpf file.
  • Run the AutoGrid program.
  • Open the output .glg file using text editor.
  • Check the output .glg file for the successful running of the AutoGrid program.


5. Running AutoDock

  • Open the PDBQT files for receptor and ligand for docking on ADT interface.
  • Perform docking run using default docking parameters.
  • Save the output as .dpf file.
  • Set docking parameters.
  • Run AutoDock.
  • Open the .dlg file to make sure the autodock run is successfully completed.


6. Analyzing Docking Runs

  • Open dlg file on the ADT panel.
  • Open and visualize conformations of ligand on ADT panel.
  • Analyze the binding energies of various conformations.
  • Change the display of ligand to sticks
  • Change the color of atoms in ligand.
  • Change the display of receptor to cartoon.
  • Change the color of residues in the receptor.
  • Analyze clusters of conformations.
  • Open dlg file with a text editor and analyze the data.
  • Export the most favorable docking pose as pdb file.


7. Visualyzing Docking using UCSF Chimera

  • Open the PDB file for the receptor on the Chimera interface.
  • Select and delete, ligand, water and glycerol molecules from the receptor structure.
  • Add the most preferred docking pose of ligand to the receptor structure.
  • Show hydrogen bonds and change the color of the bonds.
  • Show hydrogen bond length and energy.
  • Show non-bonding interactions and change the color of the pseudo-bonds.
  • Highlight the active site residues, change their display format and color.
  • Show the surface for the receptor-ligand complex colored by the amino acid hydrophobicity.
  • Show the interior of the binding pocket using the Viewing Controls in the tools menu on Chimera interface.

Contributors and Content Editors

Snehalathak

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