Difference between revisions of "AutoDock4/C2/Receptor-Preparation-for-Docking/English"

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'''Title Slide'''
 
'''Title Slide'''
−
||Welcome to this spoken tutorial on '''Receptor Preparation for Docking'''
+
||Welcome to this spoken tutorial on '''Receptor Preparation for Docking'''.
 
|-
 
|-
 
||'''Slide Number 2'''
 
||'''Slide Number 2'''
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||In this tutorial, we will learn to,
 
||In this tutorial, we will learn to,
  
−
Open the receptor pdb file on the ADT display panel.
+
Open the receptor '''pdb''' file on the '''ADT''' display panel.
  
  
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'''Learning Objectives'''
 
'''Learning Objectives'''
−
||Remove the ligand molecule crystallized along with the receptor
+
||Remove the '''ligand''' molecule crystallized along with the receptor.
  
  
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||Here I am using
 
||Here I am using
  
−
'''Ubuntu Linux '''OS version 20.04
+
'''Ubuntu Linux '''OS version 20.04.
  
−
Auto Dock Tools version 1.5.7
+
Auto Dock Tools version 1.5.7.
  
 
|-
 
|-
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'''Pre-requisites'''
 
'''Pre-requisites'''
−
||To follow this tutorial you should be familiar with,
+
||To follow this tutorial learner should be familiar with,
  
 
Topics in basic bioinformatics.
 
Topics in basic bioinformatics.
  
−
Basic operations on AutoDock Tools interface.  
+
Basic operations on '''AutoDock''' Tools interface.  
  
 
|-
 
|-
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Cursor on ADT interface.
 
Cursor on ADT interface.
−
||Open the terminal.  
+
||Let us open the terminal.  
  
−
Open AutoDock Tools interface using the terminal.
+
Open '''AutoDock''' Tools interface using the terminal.
  
  
−
At the terminal prompt type''' adt''' and press enter.
+
At the terminal prompt type ''' adt''' and press enter.
  
  
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Click on '''Remind Me Later''' button to open the '''ADT''' interface.
 
Click on '''Remind Me Later''' button to open the '''ADT''' interface.
 
|-
 
|-
−
||On the menu bar, click '''File '''> '''Read molecule'''  
+
||On the menu bar, click '''File '''> '''Read molecule.'''  
  
  
−
Cursor on''' Read molecule''' window
+
Cursor on''' Read molecule''' window.
  
  
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Click on the Open button at the bottom-right.
 
Click on the Open button at the bottom-right.
−
||On the menu bar, click on '''File '''click on '''Read molecule.'''  
+
||On the menu bar, click on '''File ''' and then click on '''Read molecule'''.
  
  
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−
Click on the '''Edit '''menu and select '''Delete water''' option.
+
Click on the '''Edit ''' menu and select '''Delete water''' option.
  
  
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Cursor on the oval button.
 
Cursor on the oval button.
−
||On the left side of the dashboard, click on a small oval button in the '''S '''column next to 2vta.
+
||On the left side of the dashboard, click on a small oval button in the '''S ''' column next to '''2vta'''.
  
  
−
This will select/deselect the atoms in the 2vta structure.
+
This will select or deselect the atoms in the '''2vta''' structure.
  
  
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Click on the OK button.
 
Click on the OK button.
−
||On the menu bar, click on '''Edit '''and '''select''' Hydrogens.  
+
||On the menu bar, click on '''Edit ''' and select '''Hydrogens'''.  
  
−
'''From the sub-menu select '''Add'''.
+
From the sub-menu select '''Add'''.
  
  
 
'''Add Hydrogens''' dialog box opens.  
 
'''Add Hydrogens''' dialog box opens.  
  
−
Select the '''All Hydrogens '''radio button.  
+
Select the '''All Hydrogens ''' radio button.  
  
 
This button is already selected for me.
 
This button is already selected for me.
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−
Chain A appears on the dashboard. Click on the small plus '''(+) '''sign on the left side of A to see the residue information.
+
Chain A appears on the dashboard.  
 +
 
 +
Click on the small plus '''(+) '''sign on the left side of A to see the residue information.
  
  
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Click on the Continue button in the pop-up.
 
Click on the Continue button in the pop-up.
−
||To delete this structure from the receptor, click on '''Edit '''on the menu bar, then '''Delete''' select''' Delete selected atoms.'''
+
||To delete this structure from the receptor, click on '''Edit '''on the menu bar.
 +
 
 +
Select '''Delete''' and then select ''' Delete selected atoms'''.
 +
 
  
 +
A warning pop up appears.
  
−
A warning pop up appears, read the message and click on the '''Continue''' button in the pop-up.
+
Read the message and click on the '''Continue''' button in the pop-up.
  
 
|-
 
|-
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||Now the receptor is ready for grid generation.
 
||Now the receptor is ready for grid generation.
 
|-
 
|-
−
||Open the '''File '''menu. Scroll down and click on''' Save''' option.  
+
||Open the '''File '''menu. Scroll down and click on ''' Save''' option.  
  
  
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−
Cursor on ''' Save Session in File dialog box. '''
+
Cursor on ''' Save Session in File''' dialog box.
−
||Let us save the receptor in the current state .
+
||Let us save the receptor in the current state.
  
  
 
Open the '''File '''menu.  
 
Open the '''File '''menu.  
  
−
Scroll down and click on''' Save''' option.  
+
Scroll down and click on ''' Save''' option.  
  
  
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−
Choose the Files of Type as ''' Pmv session files (.psf)'''.
+
Choose the Files of Type as '''Pmv session files (.psf)'''.
  
  
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−
Opened the receptor '''pdb '''file on the '''ADT''' display panel.
+
Opened the receptor '''pdb ''' file on the '''ADT''' display panel.
  
  
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Summary slide
 
Summary slide
−
||Removed the '''ligand '''molecule crystallized along with the receptor.
+
||Removed the '''ligand ''' molecule crystallized along with the receptor.
  
  

Latest revision as of 12:00, 9 November 2023

Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this spoken tutorial on Receptor Preparation for Docking.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to,

Open the receptor pdb file on the ADT display panel.


Delete the water molecules from the receptor structure.


Add hydrogens to the receptor structure.

Slide Number 3

Learning Objectives

Remove the ligand molecule crystallized along with the receptor.


Save the current session

Slide Number 4

System Requirement

Here I am using

Ubuntu Linux OS version 20.04.

Auto Dock Tools version 1.5.7.

Slide Number 5

Pre-requisites

To follow this tutorial learner should be familiar with,

Topics in basic bioinformatics.

Basic operations on AutoDock Tools interface.

Slide number 6

Code Files

The input files required for this tutorial are available in the Code files link.

Please download and extract the files.

Make a copy of all the files and then use them for practising.

Open the terminal using Show Applications menu.

At the terminal prompt type adt and press enter.


Cursor on ADT interface.

Let us open the terminal.

Open AutoDock Tools interface using the terminal.


At the terminal prompt type adt and press enter.


Give the system password when prompted.


Click on Remind Me Later button to open the ADT interface.

On the menu bar, click File > Read molecule.


Cursor on Read molecule window.


Select 2vta.pdb.


Click on the Open button at the bottom-right.

On the menu bar, click on File and then click on Read molecule.


Read molecule window opens with your default folder.


Select 2vta.pdb from the files.


Click on the Open button at the bottom-right.

Cursor on display panel. A 3D model of the receptor appears on the display panel.
Cursor on 3D model on the display panel. We need to remove solvent, ligand and refine the crystal structure.
Click on the Edit menu and select the Delete water option. To remove water molecules from the structure:


Click on the Edit menu and select Delete water option.


Water is now deleted from the structure.

Click on a small oval button in the S column next to 2vta.

Cursor on the oval button.

On the left side of the dashboard, click on a small oval button in the S column next to 2vta.


This will select or deselect the atoms in the 2vta structure.


The small oval will turn yellow.

All the atoms in the structure are highlighted as yellow dots.

On the menu bar, click on Edit >> Hydrogens >> Add.


In the Add Hydrogens dialog box, Select the All Hydrogens radio button.

Click on the OK button.

On the menu bar, click on Edit and select Hydrogens.

From the sub-menu select Add.


Add Hydrogens dialog box opens.

Select the All Hydrogens radio button.

This button is already selected for me.


By default No Bond Order and Yes radio buttons are selected.

Leave them as such.


Click on the OK button.

Zoom and show the hydrogens added to the structure. (White sticks). Now you will see the hydrogens added to the 2vta structure on the display as white sticks.
Click on the yellow oval selection button. Click on the yellow oval selection button again to deselect the protein.
Click on the small plus (+) button on the left side of 2vta on the left dashboard.

Click on the small plus (+) sign on the left side of A.


Scroll down, click on LZ1 to select.

Now we need to remove the ligand molecule crystallized along with the protein receptor.


Click on the small plus (+) button on the left side of 2vta on the left dashboard.


Chain A appears on the dashboard.

Click on the small plus (+) sign on the left side of A to see the residue information.


Scroll down to the end of the list, locate LZ11301 .


Click on the small oval button on the right side in the S column to select it.

The button becomes yellow.

Select Edit >> Delete >> Delete selected atoms.


Click on the Continue button in the pop-up.

To delete this structure from the receptor, click on Edit on the menu bar.

Select Delete and then select Delete selected atoms.


A warning pop up appears.

Read the message and click on the Continue button in the pop-up.

Cursor on the ADT panel. Now the receptor is ready for grid generation.
Open the File menu. Scroll down and click on Save option.


From the sub-menu choose Current Session.


Cursor on Save Session in File dialog box.

Let us save the receptor in the current state.


Open the File menu.

Scroll down and click on Save option.


From the sub-menu choose Current Session.


Save Session in File dialog box opens.

In the file name field, type as 2vta-receptor-prep.


Choose the Files of Type as Pmv session files (.psf).


Click on the save button in the bottom right of the dialog box.

Type the file name in the given field and save in the current working directory.


I will type the name as 2vta-receptor-prep.


Choose the Files of Type as Pmv session files (.psf).


Click on the Save button at the bottom right of the dialog box.

Open the working directory (home directory) to show the file.

Cursor on the ADT panel.

The session is saved in my working directory with the file extension .psf.

We will open this session for the grid generation process.


We will continue with the docking with the receptor grid generation in the upcoming tutorial.

Click on File menu and Exit.


In the Quit dialog box click on OK

Exit ADT by clicking on File menu and Exit.


In the Quit dialog box click on OK button.

Slide Number 7

Summary slide


With this we we come to the end of this tutorial.


Let us summarize,


In this tutorial we have,


Opened the receptor pdb file on the ADT display panel.


Deleted the water molecules from the receptor structure.


Added hydrogens to the receptor structure.


Slide Number 8

Summary slide

Removed the ligand molecule crystallized along with the receptor.


Saved the current session.

Slide Number 9



https://autodock.scripps.edu/download-autodock4/

As an assignment,


Practice the same steps with the example 1DWD given in the Examples folder in the Downloads page.

Slide Number 10


About Spoken Tutorial Project

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


Slide Number 11


Spoken tutorial workshops

  • We conduct workshops using spoken tutorials and give certificates.
  • For more details, please write to us.
Slide Number 12

Forum

Please post your timed queries in this forum.
Slide Number 13

Acknowledgement

Spoken Tutorial project was established by the 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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