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Autodock - Vina Protocol

1. The document describes a protocol for using AutoDockVina and Digital Studio Visualizer to perform molecular docking simulations and visualize the results. Key steps include preparing protein and ligand files in PDBQT format, running AutoDockVina with a configuration file, and using Digital Studio Visualizer to analyze ligand interactions and generate publication-quality images. 2. AutoDockVina docks the ligands to the protein and outputs nine files, which are then split into individual files. Digital Studio Visualizer is used to load the protein and ligand files, define the best ligand based on interactions, and produce images showing these interactions. 3. The protocol generates docked poses, allows analysis of non-covalent interactions

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Naresh kumar
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384 views12 pages

Autodock - Vina Protocol

1. The document describes a protocol for using AutoDockVina and Digital Studio Visualizer to perform molecular docking simulations and visualize the results. Key steps include preparing protein and ligand files in PDBQT format, running AutoDockVina with a configuration file, and using Digital Studio Visualizer to analyze ligand interactions and generate publication-quality images. 2. AutoDockVina docks the ligands to the protein and outputs nine files, which are then split into individual files. Digital Studio Visualizer is used to load the protein and ligand files, define the best ligand based on interactions, and produce images showing these interactions. 3. The protocol generates docked poses, allows analysis of non-covalent interactions

Uploaded by

Naresh kumar
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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AutoDockVina and Digital Studio Visualization Protocol

1. Find the target protein in Protein Data Bank (PDB) and download the PDB file in the desired
location (Keep all files same folder).
2. Open the Digital Studio Visualizer> File > Open > select the download the protein PDB file.
We will get the following:

3. Then click on water (indicated in above image) and then simply press the delete the water
molecules.
4. Click on ligand groups, it will expand the ligands present
AutoDockVina and Digital Studio Visualization Protocol

5. Then select a ligand (here we elected ligand 5), click on Define and Edit Binding Site and choose
From Current Selection. This will give the following image where a red sphere will be generated
around the selected ligand.

6. left click on the red sphere, it become yellow (below figure). Right click on yellow sphere and
then sselect Attributes. It will pop-up a window and note down the XYZ and radius values.

7. Then click File > Save As > Select the folder > Save as Protein Data Bank File (PDB). Give name
protein.
AutoDockVina and Digital Studio Visualization Protocol

8. Open ChemDraw > Draw your molecule structure > Save As “MDL Molfile (*.mol) file.

9. Then click File in Digital Studio Visualizer > Open > Select ligand’s MDL Molfile file > Save as
Protein Data Bank File (PDB) and give Name “ligand” (see below):

10. Open AutoDockTools software, click File > Read Molecule > Select the protein (PDB file) > Open
(see the below figure)
AutoDockVina and Digital Studio Visualization Protocol

11. Click Edit > Select Delete Water


12. Click Edit > Select Hydrogens > Add > Polar only > OK
13. Click Edit > Charges > Add Kollman Charges > OK

14. Click Grid > Macromolecules > Choose. This will open a pop-up window where select protein as
shown below:

After Ok, saving option will come, so save by giving name “protein.pdbqt” shown below:
AutoDockVina and Digital Studio Visualization Protocol

15. Then, click Ligand > Input > Open > select the ligand (PDB file) > open. Following image will
appear, simply click OK.

16. Click Ligand > Input > Choose > pop-up window appears > select ligand > select molecule for
AutoDock. Then click ligand > Output > Save as PDBQT > Give File name “ligand.pdbqt” > Save.

Now we have protein.pdbqt and ligand.pdbqt files. AutoDockVina use these files for docking.
AutoDockVina and Digital Studio Visualization Protocol

Now got to the folder where you have all the files:

a. Paste vina; vina_licence; vina_split files here


You can find these files in C:\Program Files (x86)\The Scripps Research Institute\Vina.

b. Prepare a note pad file naming “config”. Add the following detail in this file and save

receptor = protein.pdbqt Write the same name as you gave when preparing the pdbqt
ligand = ligand.pdbqt files of protein and ligand (step 14 and 16)

out = output.pdbqt You can give any name for out e.g., output.pddbqt or result.pdbqt

center_x = -18.420640 Write the detail obtained for XYZ in step 6.


center_y = -28.360200
center_z = 1.677040

size_x = 20.0
size_y = 20.0
size_z = 20.0

exhaustiveness = 8

c. Then in search tab of computer, type cmd and


click on Command prompt, a window appear:

d. Then, after roopa> write cd and add space and


paste address of the folder where you have all
the files.

Red part detail you can copy by selecting as shown below and then paste
AutoDockVina and Digital Studio Visualization Protocol

e. After adding above detail, click Enter.


We will get:-

Then, add the detail after HADC6> as shown below:

Then, click enter, it will start the process. The following screen will appear after completing:
AutoDockVina and Digital Studio Visualization Protocol

This will generate an out file naming output.pdbqt (as we decided its name in the config file) in the
folder. The AutoDockVina creates Nine files which is present in the output.pdbqt file.

Now we will split all these files:

Repeat the step c and d

Then add detail as shown red and click Enter:

This will split all nine docking into individual files. This will appear in the folder.

Now you can close AutoDockTool software and command prompt.


AutoDockVina and Digital Studio Visualization Protocol

17. Open the Digital Studio Visualizer, first drag the protein.pdbqt file to the Digital Studio
Visualizer. Then drag all the Nine split files to the Digital Studio Visualizer. It will generate
following screen:

Then, select ligand (here we selected ligand 2), then click Define ligand in View interaction. This
will select ligand 2. We will get the following:
AutoDockVina and Digital Studio Visualization Protocol

Click on Ligand Interactions. This will show the interactions operating between ligand and
protein residue (see the figure below)

Click the arrow indicated by red circle in the above figure. It will open a pop-up a window where
click Non-bond that give detail about all non-covalent interactions (see below).
AutoDockVina and Digital Studio Visualization Protocol

Then, you can check the interaction for other ligands just by clicking the arrow indicated by red circles.

You should choose the ligand with most H-bonds and other interactions. After selecting, the best ligand,
click Scripts > Visualization > publication Quality. We get the following:
AutoDockVina and Digital Studio Visualization Protocol

Then, click File > Save As (Image File)> Save

Select the folder where all the files are present to save

This will save your Image

This all about docking. You can play with other applications that make your data eye catching.

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