Difference between revisions of "AutoDock4/C2/Getting-Started-with-Docking/English"

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||In this tutorial, we will learn to
 
||In this tutorial, we will learn to
  
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* Download ligand and receptor files from the database.
+
* Download ligand and receptor files from the database
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* Perform ligand refinement using '''AutoDockTools'''.
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* Perform ligand refinement using '''AutoDockTools'''
 
* Prepare ligand for docking
 
* Prepare ligand for docking
 
* Save the refined ligand as a pdbqt file  
 
* Save the refined ligand as a pdbqt file  
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|-
 
|-
 
||Open the terminal using the show applications icon.
 
||Open the terminal using the show applications icon.
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||The next step is ligand refinement.
 
||The next step is ligand refinement.
  
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Type the system password.
 
Type the system password.
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||I am using the Ubuntu 20.04 system hence I will click on the '''Show Applications''' button at the bottom-left.  
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||I am using the Ubuntu 20.04 system.
 +
 
 +
Hence I will click on the '''Show Applications''' button at the bottom-left.  
  
 
On the search bar that appears I will type '''Terminal'''.  
 
On the search bar that appears I will type '''Terminal'''.  
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'''/home/snehalatha'''
 
'''/home/snehalatha'''
  
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|| Click on the red “'''Remind me later'''” button at the bottom-right corner of the window.
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|| Click on “'''Remind me later'''”.
  
  
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Select the '''mol2''' file of the ligand., '''2vta_D_LZ1.mol2'''
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Select the '''mol2''' file of the ligand, '''2vta_D_LZ1.mol2'''
  
  
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Read the message and note the information.
 
Read the message and note the information.
  
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Click on the OK button.
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Click on OK button.
 
|-
 
|-
 
|| Click on '''Edit''' menu, select '''Hydrogens''', then select '''Add''' option.
 
|| Click on '''Edit''' menu, select '''Hydrogens''', then select '''Add''' option.
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Leave all other settings as such and click on '''OK'''.
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Leave all other settings as such and click on the '''OK'''.
  
  
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In the '''Quit ''' dialog box, Do you wish to Quit?  
 
In the '''Quit ''' dialog box, Do you wish to Quit?  
  
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click on OK button.
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click on '''OK''' button.
 
|-
 
|-
 
||At the terminal prompt type '''adt''' and press Enter.
 
||At the terminal prompt type '''adt''' and press Enter.
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Click on '''Input''' then click on '''Open'''.
 
Click on '''Input''' then click on '''Open'''.
  
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Since we already saved the working directory, it is the default directory now.  
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Since we have already saved the working directory, it is the default directory now.  
  
 
|-
 
|-
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Click on '''Ligand''', and select '''Torsion Tree''' then choose ''' Torsions'''.  
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Click on '''Ligand''', and select '''Torsion Tree''' then '''Choose Torsions'''.  
  
 
'''Torsion Count''' dialog box opens.
 
'''Torsion Count''' dialog box opens.
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Saved the refined ligand structure as '''pdbqt'' file format using '''ADT'''.
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Saved the refined ligand structure as '''pdbqt''' file format using '''ADT'''.
 
|-
 
|-
 
||'''Slide Number 7'''
 
||'''Slide Number 7'''
  
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+
'''Assignment-1'''
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'''Assignment'''
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||As an assignment
 
||As an assignment
  
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https://ccsb.scripps.edu/projects/docking/
 
https://ccsb.scripps.edu/projects/docking/
 +
 
|-
 
|-
 
||'''Slide Number 8'''
 
||'''Slide Number 8'''
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 +
'''Assignment-2'''
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||
 +
 +
Download the ligand and receptor files from the PDB database  for 1DWD
 +
 +
Do the ligand refinement and  create the pdbqt file for 1DWD
 +
 +
 +
|-
 +
||'''Slide Number 9'''
  
 
'''About Spoken Tutorial Project '''
 
'''About Spoken Tutorial Project '''
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|-
 
|-
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||'''Slide Number 9'''
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||'''Slide Number 10'''
  
 
'''Spoken tutorial workshops '''
 
'''Spoken tutorial workshops '''
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|-
 
|-
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||'''Slide Number 10'''
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||'''Slide Number 11'''
  
 
'''Answers for THIS Spoken Tutorial '''
 
'''Answers for THIS Spoken Tutorial '''
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|-
 
|-
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||'''Slide 11'''  
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||'''Slide 12'''  
  
 
'''Acknowledgement '''
 
'''Acknowledgement '''

Latest revision as of 17:50, 4 September 2024

Title of script: Getting Started with Docking

Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar.

Keywords: autodock4, adt, mgl tools, ligand, receptor, rcsb protein data bank, ligand refinement, add hydrogens, detect root, rotatable bonds, pdb file, pdbqt file, video tutorial.


Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Getting Started with Docking.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to
  • Download ligand and receptor files from the database
  • Perform ligand refinement using AutoDockTools
  • Prepare ligand for docking
  • Save the refined ligand as a pdbqt file
Slide Number 3

System Requirement

Here I am using,

Ubuntu Linux OS version 20.04

AutoDockTools version 1.5.7

Google Chrome browser version 96.0.4

And a working internet connection

Slide Number 4

Pre-requisites

To follow this tutorial learner should be familiar with,

basic computer operations, and

basic bioinformatics

Open web browser, in the address bar type, 'rcsb.org


Press Enter.

https://www.rcsb.org/

Open any web browser.

We will now download the ligand and receptor files from Protein Data Bank.


In the address bar type, rcsb.org


and Press Enter


Protein Data Bank website opens.

https://www.rcsb.org/structure/2VTA


Type 2VTA in the search field.


Click on the search button.


Cursor on the page.

In the search field at the top, type the 4 letter PDB code 2VTA.


Click on the search button on the right.

The page refreshes with the 3D model and information about the protein.


2VTA codes for a Cyclin Dependent Kinase.

Cursor on the blue Download Files button.

Click the Download Files button and select PDB format.


On the right-side of the page, you will see a Download Files button.


Click on the white triangle next to the button.

From the drop down options select PDB format.

Show the pdb file, 2vta.pdb in the Downloads folder. The PDB file 2vta.pdb for the protein 2VTA downloads to your Downloads folder.
Scroll down the page,


Cursor on Small Molecules section.


Under Ligands ID, LZ1 click on Download Instance Coordinates, from the options in the drop down.

Choose MOL2 format, Chain D.

Scroll down the page, in the Small Molecules section under Ligands ID you will see LZ1.


Click on the Download Instance Coordinates drop down.

From the options in the drop down, choose MOL2 format, Chain D.

Show the mol file 2vta_D_LZ1.mol2 The mol file for the ligand downloads to the Downloads directory in my system.


Here is my Downloads directory.


Here are the two downloaded files from the PDB website, the mol file and the pdb file.

Click on the files 2vta.pdb and 2vta_D_LZ1.mol2.


Use Ctrl + X key to cut and Ctrl + V' keys to paste the files.


I will move both the downloaded files to my home directory.


I will select both the files and right-click.

From the options choose Move to option.


Select Move Destination window opens.


I will select my home folder and click on the Select button at the top-right corner.


We can alternatively use Ctrl and X keys to cut and Ctrl and V keys to paste the files.

Open the terminal using the show applications icon. The next step is ligand refinement.

Open AutoDockTools also called ADT .


I will open ADT using the terminal.

At the terminal prompt type adt and press Enter.


Type the system password.

I am using the Ubuntu 20.04 system.

Hence I will click on the Show Applications button at the bottom-left.

On the search bar that appears I will type Terminal.

Then click on the terminal option on the screen.

The terminal opens.

At the prompt I will type adt and press Enter.


Type the system password when prompted.

Cursor on ADT interface.

Click on File >> Preferences

>> Set.


In the Set User Preferences window, go to Startup Directory.


For me path is,


/home/snehalatha

Click on “Remind me later”.


ADT interface opens.


Set up your startup or working directory by going to File >> Preferences and then Set.


In the Set User Preferences window look for the Startup Directory field.


Here we need to set the path to the folder where we need to save the output files.


I am setting the path to my home directory.


Click on Make Default, and then click on Dismiss.

Click on the Ligand tab on the menu bar (last row in the menu bar)


Choose Input and then click on the Open option.

To refine the ligand, click on Ligand tab on the menu bar.


Choose Input and then click on the Open option.

In the Ligand file for AutoDock4 , open 2vta_D_LZ1.mol2 file.

Click on the Open button at the bottom-right.

The Ligand file for AutoDock4 dialog box opens.


Since I have set the path for the home directory, the folder opens by default.


We need to open mol2 file.

So select Files of Type as Mol2 files from the drop-down.


Select the mol2 file of the ligand, 2vta_D_LZ1.mol2


Click the Open button at the bottom-right.

Cursor on the display panel.

Cursor on the pop-up window.

Click on OK.

The structure will appear in the display panel on the ADT interface.


A popup window titled Summary for 2vta_D_LZ1 will appear.


The message with information about the structures will be displayed.


Read the message and note the information.

Click on OK button.

Click on Edit menu, select Hydrogens, then select Add option.


In the Add Hydrogens dialog box select radio button All Hydrogens.


Click on OK.


Cursor on the structure.

Since this structure was derived from the protein data bank, it does not contain hydrogens.


Click on the Edit menu, and select Hydrogens, then select Add option.


Add Hydrogens dialog box opens, select All Hydrogens radio button.


Leave all other settings as such and click on the OK.


You will now notice that hydrogens are added to the structure on the panel.

Slide Number 5


Adding Hydrogens

This step can be ignored in cases where the ligand structure is generated by other means such as:

quantum mechanical optimization or

draw the 2D structure and convert to 3D in Open Babel.


In the above cases the hydrogens are automatically added.

Go to File menu, >> Save >> Write PDB.


Cursor on Write options dialog box.

Type the file name as Ligand.pdb

Cursor on Browse button.

Click OK to close the dialog box.

Now we have to save this structure in pdb format.


Go to File menu select Save option.

From the sub-menu select Write PDB.


Write options dialog box opens.


File name with .pdb extension and path to my working directory will be automatically populated.


Change the file name as Ligand.pdb


You can use the BROWSE button If you want to save in any other location.


Click OK to close the dialog box.

Cursor on ADT interface. Now we need to prepare the ligand for docking.
Close the window by File >> Exit

In the Quit dialog box, Do you wish to Quit?

click on OK.

Let us close the existing ADT window.

Go to File menu and click on Exit option.


In the Quit dialog box, Do you wish to Quit?

click on OK button.

At the terminal prompt type adt and press Enter. To open a new ADT interface use the terminal as we did before.


At the terminal prompt type adt and press Enter.


Click on “Remind me later” .

ADT window opens.

Go to Ligands menu >> Input >> Open. Go to Ligands menu.

Click on Input then click on Open.

Since we have already saved the working directory, it is the default directory now.

Select Files of Type as PDB files from the drop-down.


Select Ligand.pdb, and click open.

Select Files of Type as PDB files from the drop-down.


Select Ligand.pdb, and click open button.

Cursor on the adt display panel. The structure will appear in the display panel of ADT.


A pop-up window titled summary for Ligand will appear.

Read the message and click Ok to continue.

Click Ligand >> Torsion Tree >> Detect Root.

Cursor on the green sphere on nitrogen atom.

Click Ligand and select Torsion Tree then choose Detect Root.

A green sphere will appear over the indazole Nitrogen atom.


This is the torsion root, or the center of rotation within the molecule.


This is a step to define the allowed torsions.

Click Ligand >> Torsion Tree >> Choose Torsions.

Cursor on Torsion Count dialog box.


All the bonds are red, cursor on bonds.

Click Done to close the window.

To visualize which bonds are allowed to be rotatable,


Click on Ligand, and select Torsion Tree then Choose Torsions.

Torsion Count dialog box opens.

This will change the color of all the bonds to demonstrate which are rotatable.


Here we see the number of rotatable bonds as Zero.


The parameters can be changed to fix the specific bonds.


Also allow additional degrees of freedom in ligand molecules.


Click Done to close the window.

Click Ligand >> Output >> Save as PDBQT.

A dialog box opens, file name is auto populated as ligand.pdbqt.

Click on Save button.

Save the file as a .pdbqt file.


Click on Ligand, and select Output.

Then select Save as PDBQT.


A dialog box opens, file name is auto populated as ligand.pdbqt.


Click on Save button.


This completes the step of ligand refinement using AutoDock Tools.

Slide Number 6

Summary slide

Let us summarize,


In this tutorial we have,


Downloaded ligand and receptor files from the database.


Performed the ligand refinement using AutoDockTools.


Prepared the ligand for docking.


Saved the refined ligand structure as pdbqt file format using ADT.

Slide Number 7

Assignment-1

As an assignment


Read about the docking process.


Use the link given here for more information.


https://ccsb.scripps.edu/projects/docking/

Slide Number 8

Assignment-2

Download the ligand and receptor files from the PDB database for 1DWD

Do the ligand refinement and create the pdbqt file for 1DWD


Slide Number 9

About Spoken Tutorial Project

  • The video at the following link summarizes the Spoken Tutorial project.
  • Please download and watch it.
Slide Number 10

Spoken tutorial workshops

  • We conduct workshops using spoken tutorials and give certificates.
  • For more details, please contact us.
Slide Number 11

Answers for THIS Spoken Tutorial

  • Do you have questions in THIS Spoken Tutorial?
  • Please visit this site
  • Choose the minute and second where you have the question.
  • Explain your question briefly
  • The spoken tutorial project will ensure an answer.
  • You will have to register on this website to ask questions.


Slide 12

Acknowledgement

Spoken Tutorial project was established by Ministry of Education (MoE), Govt. of India
This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.

Contributors and Content Editors

Madhurig, Snehalathak

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