View source for AutoDock4/C2/Analyzing-Docking-Runs/English

'''Title of script''': '''Analyzing Docking Runs'''


'''Author:''' Dr. Snehalatha Kaliappan and Sruthi Sudhakar


'''Keywords''': Autodock4, docking, video tutorial.


{| border=1
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|| 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 2<sup>nd</sup> 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 2<sup>nd</sup> 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 2<sup>nd</sup>.

|-
|| 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 1<sup>st</sup> 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 15'''


'''Acknowledgement '''
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.
|-
|}