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

From Script | Spoken-Tutorial
Jump to: navigation, search
Line 1: Line 1:
 +
'''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.
 +
  
 
{| border =1  
 
{| border =1  
Line 53: Line 59:
 
||Open any web browser.  
 
||Open any web browser.  
  
−
We will now download the ligand and receptor files from '''Protein Data Bank'''.
+
We will now download the '''ligand''' and '''receptor''' files from '''Protein Data Bank'''.
  
  
Line 91: Line 97:
  
  
−
||On the right-side of the page, you see a '''Download Files''' button.
+
||On the right-side of the page, you will see a '''Download Files''' button.
  
  
Line 116: Line 122:
  
  
−
Click on the '''Download Instance Coordinates '''drop down.  
+
Click on the '''Download Instance Coordinates ''' drop down.  
  
 
From the options in the drop down, choose '''MOL2 format''', '''Chain D'''.
 
From the options in the drop down, choose '''MOL2 format''', '''Chain D'''.
Line 122: Line 128:
 
|-
 
|-
 
||Show the mol file '''2vta_D_LZ1.mol2'''
 
||Show the mol file '''2vta_D_LZ1.mol2'''
−
||The mol file for the ligand downloads to the '''Downloads '''directory in my system.
+
||The mol file for the ligand downloads to the '''Downloads ''' directory in my system.
  
  
Line 142: Line 148:
 
I will select both the files and right-click.  
 
I will select both the files and right-click.  
  
−
From the options choose''' Move to''' option.
+
From the options choose ''' Move to''' option.
  
  
Line 196: Line 202:
 
'''/home/snehalatha'''
 
'''/home/snehalatha'''
  
−
||AutoDock Tools window opens.
+
|| Click on the red “'''Remind me later'''” button at the bottom-right corner of the window.
−
 
+
−
 
+
−
Click on the red “'''Remind me later'''” button at the bottom-right corner of the window.
+
  
  
Line 208: Line 211:
  
  
−
In the window, '''Set User Preferences window''' look for the '''Startup Directory ''' field.
+
In the '''Set User Preferences window''' look for the '''Startup Directory ''' field.
  
  
Line 225: Line 228:
 
Choose '''Input''' and then click on the Open option.
 
Choose '''Input''' and then click on the Open option.
  
−
||To refine the '''ligand,''' click on '''Ligand '''tab on the menu bar.  
+
||To refine the '''ligand,''' click on '''Ligand ''' tab on the menu bar.  
  
  
Line 240: Line 243:
  
  
−
We need to open '''mol2''' file so select '''Files of Type''' as '''Mol2''' files from the drop-down.
+
We need to open '''mol2''' file.
 +
 
 +
So select '''Files of Type''' as '''Mol2''' files from the drop-down.
  
  
Line 318: Line 323:
  
  
−
Go to '''File''' menu select '''Save''' option, from the sub-menu select '''Write PDB'''
+
Go to '''File''' menu select '''Save''' option.
 +
 
 +
From the sub-menu select '''Write PDB'''.
  
  
Line 345: Line 352:
 
click on '''OK'''.
 
click on '''OK'''.
  
−
||Close the existing ADT window, go to '''File''' menu and click on '''Exit''' option.
+
||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 the OK button.
+
In the '''Quit ''' dialog box, Do you wish to Quit?
 +
 
 +
click on OK button.
 
|-
 
|-
 
||At the terminal prompt type '''adt''' and press Enter.
 
||At the terminal prompt type '''adt''' and press Enter.
−
 
 
||To open a new ''' ADT''' interface use the terminal as we did before.
 
||To open a new ''' ADT''' interface use the terminal as we did before.
  
  
−
At the terminal prompt type adt and press Enter.
+
At the terminal prompt type '''adt''' and press Enter.
  
  
 
Click on “'''Remind me later'''” .  
 
Click on “'''Remind me later'''” .  
  
−
ADT window opens.
+
'''ADT''' window opens.
  
 
|-
 
|-
 
||Go to '''Ligands''' menu >> '''Input''' >> '''Open'''.
 
||Go to '''Ligands''' menu >> '''Input''' >> '''Open'''.
 +
||Go to '''Ligands''' menu.
  
−
||Go to '''Ligands''' menu, click on '''Input''' then click on '''Open'''.
+
Click on '''Input''' then click on '''Open'''.
  
 
Since we already saved the working directory, it is the default directory now.  
 
Since we already saved the working directory, it is the default directory now.  
Line 379: Line 388:
  
  
−
Select '''Ligand.pdb,''' and click '''open '''button.
+
Select '''Ligand.pdb,''' and click '''open ''' button.
 
|-
 
|-
 
||Cursor on the adt display panel.
 
||Cursor on the adt display panel.
−
||The structure will appear in the display panel of ADT.
+
||The structure will appear in the display panel of '''ADT'''.
 +
 
  
 +
A pop-up window titled''' summary for Ligand''' will appear.
  
−
A pop-up window titled''' summary for Ligand''' will appear. Read the message and click '''Ok''' to continue.  
+
Read the message and click '''Ok''' to continue.  
 
|-
 
|-
 
||Click '''Ligand''' >> '''Torsion Tree ''' >> '''Detect Root'''.
 
||Click '''Ligand''' >> '''Torsion Tree ''' >> '''Detect Root'''.
Line 413: Line 424:
  
  
−
Click on '''Ligand''', select '''Torsion Tree''' then choose ''' Torsions'''.  
+
Click on '''Ligand''', and select '''Torsion Tree''' then choose ''' Torsions'''.  
  
 
'''Torsion Count''' dialog box opens.
 
'''Torsion Count''' dialog box opens.
Line 423: Line 434:
  
  
−
The parameters can be changed to fix specific bonds.
+
The parameters can be changed to fix the specific bonds.
  
  
Line 456: Line 467:
  
 
'''Summary slide'''
 
'''Summary slide'''
−
||Let's summarize,
+
||Let us summarize,
  
  

Revision as of 15:24, 23 October 2023

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 the red “Remind me later” button at the bottom-right corner of the window.


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 the 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 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 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

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

About Spoken Tutorial Project

  • The video at the following link summarizes the Spoken Tutorial project.
  • Please download and watch it.
Slide Number 9

Spoken tutorial workshops

  • We conduct workshops using spoken tutorials and give certificates.
  • For more details, please contact us.
Slide Number 10

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 11

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

Retrieved from "https://script.spoken-tutorial.org/index.php?title=AutoDock4/C2/Getting-Started-with-Docking/English&oldid=56350"