AutoDock4/C2/Receptor-Preparation-for-Docking/English - Revision history

Snehalathak at 06:30, 9 November 2023

2023-11-09T06:30:55Z

Snehalathak at 06:26, 9 November 2023

2023-11-09T06:26:03Z

Snehalathak at 06:21, 9 November 2023

2023-11-09T06:21:22Z

Madhurig at 06:56, 8 November 2023

2023-11-08T06:56:00Z

Snehalathak at 12:14, 7 November 2023

2023-11-07T12:14:05Z

Snehalathak at 11:59, 7 November 2023

2023-11-07T11:59:14Z

Snehalathak at 11:24, 7 November 2023

2023-11-07T11:24:54Z

Snehalathak at 11:20, 7 November 2023

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Snehalathak at 11:18, 7 November 2023

2023-11-07T11:18:26Z

Snehalathak: Created page with " {| border= 1 |- || Visual Cue || Narration |- ||'''Slide Number 1''' '''Title Slide''' ||Welcome to this tutorial on '''Receptor Preparation for Docking''' |- ||'''Slide Num..."

2023-11-07T10:39:00Z

Created page with " {| border= 1 |- || Visual Cue || Narration |- ||'''Slide Number 1''' '''Title Slide''' ||Welcome to this tutorial on '''Receptor Preparation for Docking''' |- ||'''Slide Num..."

New page

{| border= 1
|-
|| Visual Cue
|| Narration
|-
||'''Slide Number 1'''

'''Title Slide'''
||Welcome to this 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 you 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.
||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 '''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/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, then '''Delete''' 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.
|-
|}

@@ Line 194: / Line 194: @@
 ||To delete this structure from the receptor, click on '''Edit '''on the menu bar.
-Select '''Delete''' then select ''' Delete selected atoms'''.
+Select '''Delete''' and then select ''' Delete selected atoms'''.
@@ Line 205: / Line 205: @@
 ||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.
@@ Line 211: / Line 211: @@
-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.
@@ Line 217: / Line 217: @@
 Open the '''File '''menu.
-Scroll down and click on''' Save''' option.
+Scroll down and click on ''' Save''' option.
@@ Line 229: / Line 229: @@
-Choose the Files of Type as ''' Pmv session files (.psf)'''.
+Choose the Files of Type as '''Pmv session files (.psf)'''.

← Older revision		Revision as of 06:26, 9 November 2023
Line 194:		Line 194:
	\|\|To delete this structure from the receptor, click on '''Edit '''on the menu bar.		\|\|To delete this structure from the receptor, click on '''Edit '''on the menu bar.

−	Select '''Delete''' select''' Delete selected atoms'''.	+	Select '''Delete''' then select ''' Delete selected atoms'''.

@@ Line 81: / Line 81: @@
 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.
@@ Line 124: / Line 124: @@
-This will select/deselect the atoms in the '''2vta''' structure.
+This will select or deselect the atoms in the '''2vta''' structure.

@@ Line 8: / Line 8: @@
 '''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'''
@@ Line 15: / Line 15: @@
 ||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.
@@ Line 27: / Line 27: @@
 '''Learning Objectives'''
-||Remove the ligand molecule crystallized along with the receptor.
+||Remove the '''ligand''' molecule crystallized along with the receptor.
@@ Line 49: / Line 49: @@
 Topics in basic bioinformatics.
-Basic operations on AutoDock Tools interface.
+Basic operations on '''AutoDock''' Tools interface.
 |-
@@ Line 62: / Line 62: @@
 Make a copy of all the files and then use them for practising.
 |-
-||Let us open the terminal using Show Applications menu.
+||Open the terminal using Show Applications menu.
 At the terminal prompt type adt and press enter.
@@ Line 68: / Line 68: @@
 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.
@@ Line 91: / Line 91: @@
 Click on the Open button at the bottom-right.
-||On the menu bar, click on '''File ''' and then click on '''Read molecule.'''
+||On the menu bar, click on '''File ''' and then click on '''Read molecule'''.
@@ Line 113: / Line 113: @@
-Click on the '''Edit '''menu and select '''Delete water''' option.
+Click on the '''Edit ''' menu and select '''Delete water''' option.
@@ Line 121: / Line 121: @@
 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/deselect the atoms in the '''2vta''' structure.
@@ Line 138: / Line 138: @@
 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'''.
@@ Line 145: / Line 145: @@
 '''Add Hydrogens''' dialog box opens.
-Select the '''All Hydrogens '''radio button.
+Select the '''All Hydrogens ''' radio button.
 This button is already selected for me.
@@ Line 175: / Line 175: @@
-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.
@@ Line 190: / Line 192: @@
 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.
-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.
 |-
@@ Line 206: / Line 212: @@
 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.
@@ Line 271: / Line 277: @@
-Opened the receptor '''pdb '''file on the '''ADT''' display panel.
+Opened the receptor '''pdb ''' file on the '''ADT''' display panel.
@@ Line 284: / Line 290: @@
 Summary slide
-||Removed the '''ligand '''molecule crystallized along with the receptor.
+||Removed the '''ligand ''' molecule crystallized along with the receptor.

← Older revision		Revision as of 12:14, 7 November 2023
Line 140:		Line 140:
	\|\|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'''.

← Older revision		Revision as of 11:59, 7 November 2023
Line 91:		Line 91:

	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.'''