Difference between revisions of "AutoDock4/C2/Analyzing-Docking-Runs/English"

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(Created page with " '''Title of script''': '''Analyzing Docking Runs''' '''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar''' '''Keywords: Autodock4, docking, video tutorial.''' {|...")
 
 
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'''Title of script''': '''Analyzing Docking Runs'''
 
'''Title of script''': '''Analyzing Docking Runs'''
  
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'''Author:''' Dr. Snehalatha Kaliappan and Sruthi Sudhakar
  
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'''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar'''
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'''Keywords''': Autodock4, docking, video tutorial.
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'''Keywords: Autodock4, docking, video tutorial.'''
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Analyze the binding energies of various conformations
 
Analyze the binding energies of various conformations
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|| The inputfiles required for this tutorial are available in the '''Code files''' link.
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|| The input files required for this tutorial are available in the '''Code files''' link.
 
* Please download and extract the files.
 
* Please download and extract the files.
  
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|| Save the input files in your home directory or working directory
 
|| Save the input files in your home directory or working directory
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Make a copy of all the files and then use them for practising  
 
Make a copy of all the files and then use them for practising  
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|-
 
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||  I have opened the '''AutoDock Tools '''interface.
 
||  I have opened the '''AutoDock Tools '''interface.
  
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Let us analyze the dlg file generated during the autodock run.
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Let us analyze the '''dlg''' file generated during the autodock run.
  
 
|-
 
|-
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Click '''OK''' to close the pop-up.
 
Click '''OK''' to close the pop-up.
  
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||A warning pop-up opens. Read the message shown on the pop-up.
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||A warning pop-up opens.  
 +
 
 +
Read the message shown on the pop-up.
  
 
It gives information about the number of docked conformations.  
 
It gives information about the number of docked conformations.  
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'''From '''the sub-menu choose''' Load.'''
 
'''From '''the sub-menu choose''' Load.'''
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|| To visualize the docking results, click on '''Analyze '''again.  
+
|| To visualize the docking results, click on '''Analyze ''' again.  
  
  
 
From the drop-down choose '''Conformations'''.
 
From the drop-down choose '''Conformations'''.
  
−
From the sub-menu choose '''Load.'''
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From the sub-menu choose '''Load'''.
 
|-
 
|-
 
|| Cursor on '''2vta Conformation Chooser '''table.
 
|| Cursor on '''2vta Conformation Chooser '''table.
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|| Close the window.
 
|| Close the window.
 
|-
 
|-
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|| Click on''' Analyze '''on the menu bar and select '''Macromolecule f'''rom the dropdown.''' '''
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|| Click on''' Analyze '''on the menu bar and select '''Macromolecule '''from the dropdown.''' '''
  
 
Select '''Open''' from the sub-menu.
 
Select '''Open''' from the sub-menu.
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|| Click on''' Analyze '''on the menu bar.  
 
|| Click on''' Analyze '''on the menu bar.  
  
−
Select '''Macromolecule f'''rom the dropdown.''' '''
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Select '''Macromolecule '''from the dropdown.''' '''
  
 
From the sub-menu select '''Open'''.
 
From the sub-menu select '''Open'''.
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|| Let us visualize the ligand clearly.
 
|| Let us visualize the ligand clearly.
  
−
We can change the display from lines display to '''sticks '''display.
+
We can change the display from lines display to '''sticks '''.
  
 
In the left panel, click on the oval button on column '''B''' for the ligand.  
 
In the left panel, click on the oval button on column '''B''' for the ligand.  
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Click on '''close''' at the bottom to close the window.
 
Click on '''close''' at the bottom to close the window.
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|| Click on the triangle button in the last column '''CL.'''
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|| Click on the triangle button in the last column '''CL'''.
  
 
A menu opens at the bottom of the panel.
 
A menu opens at the bottom of the panel.
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We will proceed with the selection.
 
We will proceed with the selection.
  
−
In the coloring '''Scheme panel''', I will select '''By atom type.'''
+
In the '''Coloring Schemes panel''', I will select '''By atom type.'''
  
  
−
Now we can see the ligand as sticks display and elements in '''Rasmol colors.'''  
+
Now we can see the ligand as sticks display and elements in '''Rasmol colors'''.
  
  
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|| By default the receptor is displayed as lines.  
 
|| By default the receptor is displayed as lines.  
  
−
In the left panel, In the '''2vta '''row, click on the oval button in column''' R.'''  
+
In the left panel, In the '''2vta '''row, click on the oval button in column''' R''' .
  
 
Observe the panel, the receptor is now displayed as ribbons.
 
Observe the panel, the receptor is now displayed as ribbons.
  
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Uncheck the oval button on column''' L''' to hide the lines display.
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Uncheck the oval button on column ''' L''' to hide the lines display.
  
 
|-
 
|-
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We will proceed with the selection.
 
We will proceed with the selection.
  
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From the list of options, select '''By rainbow.'''
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From the list of options, select '''By rainbow'''.
  
 
The receptor is now seen in rainbow colors.
 
The receptor is now seen in rainbow colors.
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Cursor on the '''ligand '''menu.  
 
Cursor on the '''ligand '''menu.  
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|| Click on '''Analyze''', select '''Conformations '''from the drop-down.
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|| Click on '''Analyze''', select '''Conformations ''' from the drop-down.
  
 
Then select '''play, ranked by energy…'''..  
 
Then select '''play, ranked by energy…'''..  
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|| Click on the 2<sup>nd</sup> last button on the ligand menu bar to change play options.
 
|| Click on the 2<sup>nd</sup> last button on the ligand menu bar to change play options.
  
−
A pop-up dialog-box '''Set play options '''opens.
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A pop-up dialog-box '''Set Play options '''opens.
  
 
Check the check-box for '''Show Info''' at the top.
 
Check the check-box for '''Show Info''' at the top.
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Cursor on '''Hydrogen Bonds''' pop-up window.  
 
Cursor on '''Hydrogen Bonds''' pop-up window.  
  
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|| In the '''Set play options '''dialog, check the check-box for''' Build H-bonds'''.
+
|| In the '''Set play options '''dialog, check the check-box for ''' Build H-bonds'''.
  
 
This will open another pop-up, '''Hydrogen Bonds'''.  
 
This will open another pop-up, '''Hydrogen Bonds'''.  
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Zoom-in the structure on the panel.
 
Zoom-in the structure on the panel.
  
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|| Only one amino acid''' Phenylalanine146 '''is hydrogen bonded to the ligand in this conformation.
+
|| Only one amino acid ''' Phenylalanine146 ''' is hydrogen bonded to the ligand in this conformation.
  
 
Zoom-in the structure on the panel.
 
Zoom-in the structure on the panel.
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Here for conformation 1 the distance is 2.237 angstroms.
 
Here for conformation 1 the distance is 2.237 angstroms.
  
−
Now uncheck the checkbox for '''Show Distance'''.
+
Now uncheck the checkbox for '''Show Distances'''.
  
 
To view the hydrogen bond energies, check the check-box for''' Show Energy.'''
 
To view the hydrogen bond energies, check the check-box for''' Show Energy.'''
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Cursor on the values.
 
Cursor on the values.
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|| These conformations are ranked lowest to highest energy.
+
|| These conformations are ranked from lowest to highest energy.
  
 
More negative binding energy with a good pose in the active site would be one of the most favorable poses.  
 
More negative binding energy with a good pose in the active site would be one of the most favorable poses.  
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Scroll down to the “CLUSTER ANALYSIS OF CONFORMATIONS” section
 
Scroll down to the “CLUSTER ANALYSIS OF CONFORMATIONS” section
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||  I will open the''' 2vta.dlg '''file saved in the home folder using any text editor.
+
||  I will open the ''' 2vta.dlg '''file saved in the home folder using any text editor.
  
 
Read the information given here.
 
Read the information given here.
  
−
Scroll down to the '''CLUSTER ANALYSIS OF CONFORMATIONS '''section.  
+
Scroll down to the '''CLUSTER ANALYSIS OF CONFORMATIONS ''' section.  
 
   
 
   
  
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The '''RMSD''' table gives information about:
 
The '''RMSD''' table gives information about:
  
−
ranking, sub-ranking and Binding energy information for all the 10 conformations.
+
ranking, sub-ranking and Binding energy for all the 10 conformations.
 
|-
 
|-
 
|| Cursor on ADT interface.
 
|| Cursor on ADT interface.
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Save this docking pose as a pdb file by clicking on '''File '''menu.
 
Save this docking pose as a pdb file by clicking on '''File '''menu.
  
−
Select '''Save''' from the drop-down. From the sub-menu, select '''Write PDB'''.
+
Select '''Save''' from the drop-down.  
 +
 
 +
From the sub-menu, select '''Write PDB'''.
  
 
|-
 
|-
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|| This brings us to the end of this tutorial.
 
|| This brings us to the end of this tutorial.
  
−
Let's summarize,  
+
Let us summarize,  
  
 
|-
 
|-
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Opened the dlg file using a text editor and analyzed the data.
 
Opened the dlg file using a text editor and analyzed the data.
  
−
Exported the most favorable docking pose as pdb file.
+
Exported the most favorable docking pose as a pdb file.
 
|-
 
|-
 
|| '''Slide Number 10'''
 
|| '''Slide Number 10'''
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* Please download and watch it.  
 
* Please download and watch it.  
 
|-
 
|-
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|| '''Slide''' '''Number 12'''
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|| '''Slide Number 12'''
  
  
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* For more details, please write to us.  
 
* For more details, please write to us.  
 
|-
 
|-
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|| '''Slide''' '''Number 13'''
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|| '''Slide Number 13'''
  
  
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||  Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
 
||  Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
 
|-
 
|-
−
|| '''Slide''' '''Number 15'''
+
|| '''Slide''' '''Number 14'''
  
  

Latest revision as of 17:44, 7 June 2024

Title of script: Analyzing Docking Runs

Author: Dr. Snehalatha Kaliappan and Sruthi Sudhakar

Keywords: Autodock4, docking, video tutorial.


Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this spoken tutorial on Analyzing Docking Runs.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to

Open the dlg file on the ADT panel

Open and visualize the most favorable conformations of the ligand

Analyze the binding energies of various conformations


Slide Number 3

Learning Objectives

Analyze clusters of conformations

Open the dlg file with using a text editor and analyze the data

Export the most favorable docking pose as a pdb file.

Slide Number 4

System Requirement

Here I am using,

Ubuntu Linux OS version 20.04

AutoDockTools version 1.5.7


gedit version 3.36.2

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.
Slide number 7

Code Files

Save the input files in your home directory or working directory

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

Open ADT interface using the terminal. I have opened the AutoDock Tools interface.

Let us analyze the dlg file generated during the autodock run.

Click on Analyze on the menu bar,

from the drop-down choose Dockings.


Click Open from the sub menu.

Click on Analyze on the menu bar.


From the drop-down choose Dockings.


Click Open from the sub menu.

Cursor on Docking Log File window.


Select 2vta.dlg from the list of files.


Click on Open button.

Docking Log File window opens.


Select 2vta.dlg from the list of files from your working directory.


Click on the Open button.

Cursor on the pop-up window.

Read the information.

Click OK to close the pop-up.

A warning pop-up opens.

Read the message shown on the pop-up.

It gives information about the number of docked conformations.

It is 10 for the present example.

It gives information on how to view the conformations.


Click the OK button to close the pop-up.

Click on Analyze, from the drop-down choose Conformations.

From the sub-menu choose Load.

To visualize the docking results, click on Analyze again.


From the drop-down choose Conformations.

From the sub-menu choose Load.

Cursor on 2vta Conformation Chooser table. 2vta Conformation Chooser window opens.

In this table, the lower panel has conformations numbered.

You can also see the corresponding docked energy values.

Click on 1-1 conformation from the list.


Cursor on the top panel.

Click on any conformation number in the list.

The top panel now shows:

Binding energy

kI, inhibition constant

Internal energy

Torsional energy etc.

Click “x” on top-right to close the window. Close the window.
Click on Analyze on the menu bar and select Macromolecule from the dropdown.

Select Open from the sub-menu.

Cursor on the receptor.

Zoom-in and show the ligand.

Click on Analyze on the menu bar.

Select Macromolecule from the dropdown.

From the sub-menu select Open.

The receptor is now displayed as lines on the panel.

Zoom-in to see the receptor-ligand complex.

In the left panel, click on oval button on column B for the ligand. Let us visualize the ligand clearly.

We can change the display from lines display to sticks .

In the left panel, click on the oval button on column B for the ligand.

The ligand is now displayed in sticks model.

Unselect lines display by clicking on the red oval in column L.

Click on the triangle button in the last column CL in the ligand row.

Select By atom type.

Click on close at the bottom to close the window.

Click on the triangle button in the last column CL.

A menu opens at the bottom of the panel.

By default All Representations

and balls and sticks check-boxes are checked.

Leave them as such.

We will proceed with the selection.

In the Coloring Schemes panel, I will select By atom type.


Now we can see the ligand as sticks display and elements in Rasmol colors.


Click on close at the bottom to close the window.

Cursor on the receptor.

Click on oval button on column R to display receptor as ribbons .

Uncheck the oval button on column L to hide the sticks display.

By default the receptor is displayed as lines.

In the left panel, In the 2vta row, click on the oval button in column R .

Observe the panel, the receptor is now displayed as ribbons.

Uncheck the oval button on column L to hide the lines display.

Click on the triangle button in the last column CL in the receptor row.

Select By rainbow.

Click on close at the bottom to close the window.

To make the display colorful, click on the triangle button in the last column CL

A menu opens at the bottom of the left panel.

By default All Representations and Secondarystructure check-boxes are checked.

We will proceed with the selection.

From the list of options, select By rainbow.

The receptor is now seen in rainbow colors.

Users can explore the other options given in the list.

Click on close at the bottom to close the window.

Cursor on the panel. We can also view the conformations of ligand ranked by energy, from lowest to highest.
Again click on Analyze on the menu bar. Select Conformations from the drop -down.

Select play, ranked by energy…..

Cursor on the ligand menu.

Click on Analyze, select Conformations from the drop-down.

Then select play, ranked by energy…..

A menu titled ligand opens with various button options to play.

Click on the white arrow play button, on the ligand menu.

Cursor on the panel.

Click on the white forward arrow play button on the ligand menu bar.

On the panel, the 10 conformations are played one after the other in a sequence.

Cursor on the “ligand” bar.

Click on the small black arrow buttons to play.

Click on the white backward arrow on the ligand menu to play the conformations in reverse sequence.

This brings the ligand conformation display back to zero.

Conformation number zero represents the initial coordinates of ligand pdbqt that we had used for docking.

Click on the small black forward arrow button to play conformations one-by-one.

I will bring conformation 1 back on the panel by clicking on the black backward button.

Click on the 2nd last button (&)on the “ligand” bar.

In the Set play options dialog, check the check-box for Show Info at the top.

Click on the 2nd last button on the ligand menu bar to change play options.

A pop-up dialog-box Set Play options opens.

Check the check-box for Show Info at the top.


Cursor on Input Conformation pop-up box.

Binding energy,ligand efficiency, inhibition constant, and other parameters are listed here


Click on the X top-right to close the pop-up.

Another pop-up box called Conformation 1 info opens.


It gives information of the particular conformation.

Read the information.

Conformation number 1 has the binding energy of -5.66.

The inhibition constant value for this conformation is also given in the information pop-up

Close the Conformation 1 Info

pop-up box.

In the Set play options dialog,

check the check-box for Build H-bonds.

Cursor on Hydrogen Bonds pop-up window.

In the Set play options dialog, check the check-box for Build H-bonds.

This will open another pop-up, Hydrogen Bonds.

This will show the information of hydrogen bonds for the particular conformation.

Cursor on Hydrogen Bonds pop-up window.

Zoom-in the structure on the panel.

Only one amino acid Phenylalanine146 is hydrogen bonded to the ligand in this conformation.

Zoom-in the structure on the panel.

In the Hydrogen Bonds pop-up, check the check-box for Show Distances.

Check-box for Show Energy and uncheck the checkbox for Show Distance.

In the Hydrogen Bonds pop-up, check the check-box for Show Distances if it is not checked.

Here for conformation 1 the distance is 2.237 angstroms.

Now uncheck the checkbox for Show Distances.

To view the hydrogen bond energies, check the check-box for Show Energy.

Cursor on the panel. On the panel you can see the hydrogen bond energy as -3.069.
Click the black arrow button to go to conformation number one.

Cursor on the values.

I will click the black arrow button to go to conformation number 2.

In the Hydrogen Bonds pop-up, check the check-box for Show Distances.

On the panel we can see hydrogen bond distance as 2.103 angstroms.

In the conformation 2 info pop up:

The binding energy is -5.66.

It shows the same binding energy as the previous conformation which was ranked one.


The inhibition constant is 71.01.

Notice that this conformation has a slightly higher inhibition constant when compared to conformation number 1.

Hence it is ranked 2nd.

Click on the front black arrow again.

Cursor on the values.

Click on the black play button for all the conformations.

You can see the energies and hydrogen bond information of all the conformations.

Text annotation.

(A conformer with -10.5 Kcal better than one with -7kcal)

Cursor on the values.

These conformations are ranked from lowest to highest energy.

More negative binding energy with a good pose in the active site would be one of the most favorable poses.

Cursor on the values. Bring the most favorable pose, that is conformation 1 back on the panel.

Close all the pop up windows.

Cursor on the panel. Let us now view the clustering.
Click on Analyze on the menu bar again and select Clusterings option.

Cursor on Ligand Clusterning window.

Click on Analyze on the menu bar again and select Clusterings option.

Select Show option from the sub- menu.

Ligand Clustering window opens.

Here you can see the 10 conformations grouped into 2 clusters.

There are 8 conformations grouped in one cluster and 2 conformations in another cluster.

Table is in the form of a 2D histogram.

Open the 2vta.dlg file.

Scroll down to the “CLUSTER ANALYSIS OF CONFORMATIONS” section

I will open the 2vta.dlg file saved in the home folder using any text editor.

Read the information given here.

Scroll down to the CLUSTER ANALYSIS OF CONFORMATIONS section.


The number of conformations is 10.

The 10 conformations are grouped into 2 clusters according to the similarity in their structure.

Cursor on Clustering Histogram table. Clustering Histogram table gives more information.

There are 8 conformations grouped in cluster 1 and 2 conformations in Cluster 2.

Cursor on the value. The lowest binding energy -5.66 is for Run 4, which is ranked number 1.

Hence this is the most preferred conformation.

Scroll down to the RMSD table. Scroll down to RMSD table.

The RMSD table gives information about:

ranking, sub-ranking and Binding energy for all the 10 conformations.

Cursor on ADT interface.

Click on the black forward arrow to play conformer 1.

Back to the ADT interface.

We will save the most favorable pose as a pdb file.

Play the conformation ranked one.

This is the most favorable conformation among the 10 poses.

Click on the yellow oval in column S for the ligand.

Select Save from the drop-down. From the sub-menu, select Write PDB.

Select the ligand by clicking the small oval on the ligand row S column, that is 1st column on the left panel.

Save this docking pose as a pdb file by clicking on File menu.

Select Save from the drop-down.

From the sub-menu, select Write PDB.

Curson on Write Options dialog box.

Type file name as ligand-conf1.pdb.


Write Options dialog box opens.

Filename field is already populated with path and filename.

You can choose to save it at a different location by clicking on the Browse button.

I will not change the path, but change the file name to ligand-conf1.pdb.

Click on the OK button at the bottom of the dialog box.

Cursor on the panel. To save another conformation, you can repeat this procedure.

Change the number in the ligand button menu to 2.

Close all the windows.

Select again and Save as PDB using the File menu.

I will save the file as ligand-conf2.pdb

Show home folder, cursor on ligand-con1.pdb and ligand-con2.pdb files.

Cursor on ligand-con1.pdb file.

The pdb files, ligand-con1.pdb and ligand-con2.pdb are saved in the home folder.

These files can be read by Pymol, Chimera or Jmol for further analysis and for the generation of high-resolution images.

Only Narration This brings us to the end of this tutorial.

Let us summarize,

Slide Number 8

Summary

In this tutorial, we,

Opened the dlg file on the ADT panel.

Opened and visualize the most favorable conformations of ligand.

Analyzed the binding energies of various conformations.

Slide Number 9

Summary

Analyzed clusters of conformations.

Opened the dlg file using a text editor and analyzed the data.

Exported the most favorable docking pose as a pdb file.

Slide Number 10

Assignment

As an assignment,

Analyze the dlg files generated for 1DWD receptor-ligand complex.

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

Slide Number 11


About Spoken Tutorial Project

  • The video at the following link summarizes the Spoken Tutorial project.
  • Please download and watch it.
Slide Number 12


Spoken tutorial workshops

  • We conduct workshops using spoken tutorials and give certificates.
  • For more details, please write to us.
Slide Number 13


Forum

  • Please post your timed queries in this forum.
Slide Number 14

Acknowledgement

Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
Slide Number 14


Acknowledgement

This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Contributors and Content Editors

Madhurig, Snehalathak

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