Molecular Docking Using Autodock

How to use Autodock and Autodock vina?

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Molecular Docking using
Autodock 4


Sapan K. Shah
Asst. Prof.
Priyadarshini J. L. College
of Pharmacy, Nagpur

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What is Docking?
Molecular docking is a study of
how two or more molecular
structures, eg. drug and receptor,
match along to be a perfect fit
(Gane & Dean, 2000).
“Predicting the best ways two
molecules will interact.
•Obtain the 3D structures of
the two molecules.
•Locate the best binding site.
•Determine the best binding
modes

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1. Download and Installation of AutoDock
3. How to prepare a ligand file for AutoDock 4
2. How to prepare a receptor file for AutoDock4
4. How to prepare a grid parameter file for AutoGrid 4
5. How to prepare a docking parameter file for AutoDock4
6. How To Run AutoDock?
7. How To Analyse AutoDock Results
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•AutoDock is a suite of automated docking
tools. It is designed to predict how small
molecules, bind to a receptor of known 3D
structure.
•Two generations of software: AutoDock 4
and AutoDock Vina
Download and Installation of AutoDock
Step 1
Download a new executable from:
http://autodock.scripps.edu/downloads

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How to prepare a receptor file for AutoDock4 Step 2
1.Download Protein Data Bank
https://www.rcsb.org/
2.Fetch Protein data file
directly
File / Open…target.pdb
Delete water molecules
GO TO AUTODOCK
Add Hydrogen/Add Polar Only
Remove unwanted residue
Add Charges-
1)Kollman charge
2)Compute Gasteiger charges
Assign hydrogen-AD4 type only
Save as ….target.pdbqt

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How to prepare a ligand file for AutoDock 4
Draw and save as mol2 or pdb file
1.Zinc database:
http://zinc12.docking.org/
2.Drug bank:
https://www.drugbank.ca/
3.PubChem:
https://pubchem.ncbi.nlm.nih.gov/#query=aspirin
4.Chemspider
http://www.chemspider.com/
5.ChemDB
http://cdb.ics.uci.edu/
6.ChemMBL
https://www.ebi.ac.uk/chembl/
7.Using Avogadro- My favorite

LIGAND /
INPUT /
OPEN

SAVE AS..
ligand.pdbqt
LIGAND /
OUTPUT
GO TO
AUTODOCK
Step 3

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*Source: NPTEL/CADD

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How to prepare a grid parameter file for AutoGrid 4
Step 4
Grid map optimization

Select Grid / Macromolecule / Choose..target……Save as
target.pdbqt
Select Grid /Grid box…… Grid Parameters….File / close
saving current
Grid /Output / Save target.gpf …… target.gpf

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How to prepare a docking parameter file for AutoDock4




Docking /Macromolecule /
Set rigid filename
Docking /Ligand / Choose…ligand
Docking /Search parameters /
Genetic algorithm. Accept Docking /Docking
parameters…accept
Docking /Output / Lamarckian…. Save
target.dpf
Step 5

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How To Run AutoDock? Step 6
Run Autogrid
•Select tab RUN>>RUN AUTOGRID>>Click BROWSE>>Select AUTOGRID APPLICATION FILE in PROGRAM PATH
NAME>>Click BROWSE>>Select TARGET.GPF in PARAMET FILE NAME>>Click LAUNCH
Run Autodock
•Select tab RUN>>RUN AUTODOCK>>Click BROWSE>>Select AUTODOCK APPLICATION FILE in PROGRAM PATH
NAME>>Click BROWSE>>Select TARGET.DPF in PARAMET FILE NAME>>Click LAUNCH
Run Autodock Vina
•OPEN COMMAND PROMPT
•Type “C: foldername“ for selecting path
•Type "C:\Program Files (x86)\The Scripps Research Institute\Vina\Vina.exe" --
receptor target.pdbqt --ligand ligand.pdbqt --config conf.txt --log log.txt --out
output.pdbqtxt]

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How To Analyse AutoDock Results Step 7
Analyse / Docking
/ Open/target.dlg
Analyse /
Macromolecule /
Choose/target
Analyse /
Conformations /
Play….

show
conformations
Analyse /
openautodockvina
results/
Open/outputfile

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