Difference between revisions of "AutoDock4/C2/Visualizing-Docking-using-UCSF-Chimera/English"

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'''Title Slide'''
 
'''Title Slide'''
−
|| Welcome to this spoken tutorial on '''Visualizing Docking using UCSF Chimera.'''
+
|| Welcome to this spoken tutorial on '''Visualizing Docking using UCSF Chimera'''.
  
 
|-
 
|-
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|| Here I am using,
 
|| Here I am using,
  
−
'''Ubuntu Linux '''OS version 20.04
+
'''Ubuntu Linux ''' OS version 20.04
  
−
AutoDockTools version 1.5.7
+
'''AutoDockTools''' version 1.5.7
  
−
UCSF Chimera version 1.17.2
+
'''UCSF Chimera''' version 1.17.2
  
 
|-
 
|-
Line 76: Line 76:
 
topics in basic bioinformatics
 
topics in basic bioinformatics
  
−
basic operations on UCSF Chimera interface.
+
basic operations on '''UCSF Chimera''' interface.
  
−
Please refer to the link below for tutorials on UCSF Chimera series.
+
Please refer to the link below for tutorials on '''UCSF Chimera''' series.
  
 
|-
 
|-
Line 170: Line 170:
 
Cursor on '''GOL, HOH''' and '''LZ1.'''
 
Cursor on '''GOL, HOH''' and '''LZ1.'''
  
−
|| Click on '''Select '''menu, from the drop-down select '''Residue '''option.
+
|| Click on '''Select ''' menu, from the drop-down select '''Residue ''' option.
  
−
The sub-menu shows 3 residues under the A'''ll nonstandard''' category.
+
The sub-menu shows 3 residues under the '''All nonstandard''' category.
  
−
'''GOL, HOH '''and''' LZ1''', that is, '''glycerol''', water and '''Indazole''' respectively.
+
'''GOL''', '''HOH ''' and ''' LZ1''', that is, '''glycerol''', water and '''Indazole''' respectively.
  
 
|-
 
|-
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|-
 
|-
−
 
 
|| Cursor on glycerol structure.
 
|| Cursor on glycerol structure.
  
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|| Glycerol molecules get highlighted on the panel in green color.
 
|| Glycerol molecules get highlighted on the panel in green color.
  
−
Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''  
+
Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds'''.
  
 
From the sub-menu select the '''delete''' option.
 
From the sub-menu select the '''delete''' option.
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|-
 
|-
−
 
 
|| Click on the '''Select '''menu.
 
|| Click on the '''Select '''menu.
  
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|-
 
|-
−
 
 
|| Cursor on the panel.
 
|| Cursor on the panel.
 
|| To this receptor structure we will add the best pose conformation of the ligand obtained by '''autodock runs'''.
 
|| To this receptor structure we will add the best pose conformation of the ligand obtained by '''autodock runs'''.
Line 238: Line 235:
  
 
Click on the '''Open''' button at the bottom of the dialog box.
 
Click on the '''Open''' button at the bottom of the dialog box.
−
 
−
 
 
|| From the '''File''' menu, select '''Open''' option.
 
|| From the '''File''' menu, select '''Open''' option.
  
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From the list of files select the '''pdb''' file containing the best pose of the ligand from the '''autodock runs'''.
 
From the list of files select the '''pdb''' file containing the best pose of the ligand from the '''autodock runs'''.
  
−
We had saved this file earlier as '''ligand-conf1.pdb.'''
+
We had saved this file earlier as '''ligand-conf1.pdb'''.
  
  
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|-
 
|-
−
 
 
||  '''Slide Number 9'''
 
||  '''Slide Number 9'''
  
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* hydrogen bonds and  
 
* hydrogen bonds and  
−
* other polar and no n-polar interactions can be visualized.
+
* other polar and non-polar interactions can be visualized.
  
 
We can also visualize the active site pocket and surface properties of the receptor.
 
We can also visualize the active site pocket and surface properties of the receptor.
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'''Active Site Residues'''
 
'''Active Site Residues'''
 +
 +
Lys33, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Asp86, Leu134, and Asp145.
  
 
|| From the literature, the following residues form much of the ligand binding pocket:  
 
|| From the literature, the following residues form much of the ligand binding pocket:  
−
 
−
Lys33, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Asp86, Leu134, and Asp145.
 
  
 
Let us highlight these residues in the structure on the panel.
 
Let us highlight these residues in the structure on the panel.
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|| Cursor on the panel.
 
|| Cursor on the panel.
 
|| Back to the '''Chimera''' interface.
 
|| Back to the '''Chimera''' interface.
−
 
  
 
We will use the command line to select and highlight the active site residues.
 
We will use the command line to select and highlight the active site residues.
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|-
 
|-
−
 
 
|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.
 
|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.
−
|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.  
+
|| Select '''Atoms/Bonds''', choose '''Show ''' from the sub-menu.  
  
 
Atoms are now displayed as sticks for the '''lysine'''.
 
Atoms are now displayed as sticks for the '''lysine'''.
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|-
 
|-
−
 
 
|| Actions menu again and select the colors option.
 
|| Actions menu again and select the colors option.
  
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Select '''by element''' from the sub menu.
 
Select '''by element''' from the sub menu.
  
−
On the panel you can see the '''ball and stick''' model in '''rasmol '''color coding of elements.
+
On the panel you can see the '''ball and stick''' model in '''rasmol ''' color coding of elements.
  
−
Click on '''Select '''option and clear the selection.
+
Click on '''Select ''' option and clear the selection.
  
 
|-
 
|-
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At the command line edit the command as shown.
 
At the command line edit the command as shown.
  
−
Delete number 33.A  
+
Delete the number 33.A  
  
 
and in its place type 80.A, rest of the command remains as such.
 
and in its place type 80.A, rest of the command remains as such.
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−
Go to '''Actions''' menu and click on '''Show''', '''Phenylalanine 80''' is shown in sticks display.
+
Go to '''Actions''' menu and click on '''Show'''.
 +
 
 +
'''Phenylalanine 80''' is shown in sticks display.
  
  
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|-
 
|-
−
 
 
||  Click on the '''Tools '''menu.  
 
||  Click on the '''Tools '''menu.  
  
−
Select '''Structure Analysis''' from the sub-menu choose''' FindHBond '''option.
+
Select '''Structure Analysis'''.
 +
 
 +
From the sub-menu choose''' FindHBond '''option.
  
 
|| Click on the '''Tools '''menu.  
 
|| Click on the '''Tools '''menu.  
  
−
Select '''Structure Analysis, '''from the sub-menu choose''' FindHBond '''option.
+
Select '''Structure Analysis'''.
 +
 
 +
From the sub-menu choose''' FindHBond''' option.
  
 
|-  
 
|-  
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* Click on the check box against '''Label Hydrogen bond with distance'''.
 
* Click on the check box against '''Label Hydrogen bond with distance'''.
−
* Click on '''Only find H-bonds, with at least one end selected.'''
+
* Click on '''Only find H-bonds, with at least one end selected'''.
  
  
−
Uncheck any other check boxes if checked.* And click on '''Write in formation to reply log'''.
+
Uncheck any other check boxes if checked.
 +
* And click on '''Write in formation to reply log'''.
  
 
Click on '''Apply''' and '''OK''' buttons.
 
Click on '''Apply''' and '''OK''' buttons.
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|| Observe the panel.
 
|| Observe the panel.
  
−
'''Hydrogen bonds''' are shown as '''pseudo'''-bonds of specified color and line width.
+
'''Hydrogen bonds''' are shown as '''pseudo-bonds''' of specified color and line width.
  
 
Here we can see only two hydrogen bonds with '''indazole'''.  
 
Here we can see only two hydrogen bonds with '''indazole'''.  
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|| Details of the bonds can be viewed on the '''Reply log'''.
 
|| Details of the bonds can be viewed on the '''Reply log'''.
  
−
Open '''Reply log '''using '''Favorites''' menu.
+
Open '''Reply log ''' using '''Favorites''' menu.
  
 
Click on '''Favorites''' menu.
 
Click on '''Favorites''' menu.
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Click on the color box.
 
Click on the color box.
  
−
In the '''Color Editor '''window I will select green.  
+
In the '''Color Editor ''' window I will select green.  
  
 
Close the color selector.
 
Close the color selector.
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Observe the panel.
 
Observe the panel.
  
−
All the contacts of ligand''' LZ1 '''are shown as green lines.  
+
All the contacts of ligand''' LZ1 ''' are shown as green lines.  
  
 
|-
 
|-

Revision as of 12:42, 19 June 2024


Title of script: Visualizing Docking using UCSF Chimera

Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar

Keywords: Autodock4, docking, UCSF Chimera, receptor, ligand, residues, hydrogen bonds, video tutorial.


Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this spoken tutorial on Visualizing Docking using UCSF Chimera.
Slide Number 2


Learning Objectives

In this tutorial, we will,

Open the PDB file for the receptor on the Chimera interface.

Select and delete solvent and other residues from the receptor structure.

Slide Number 3


Learning Objectives

Add the most preferred docking pose of the ligand to the receptor structure.


Show hydrogen bonds and other interactions.

Slide Number 4


Learning Objectives

Highlight the active site residues.


Show the receptor-ligand surface and active site pocket.

Slide Number 5

System Requirement

Here I am using,

Ubuntu Linux OS version 20.04

AutoDockTools version 1.5.7

UCSF Chimera version 1.17.2

Slide Number 6

Pre-requisites


https://spoken-tutorial.org/tutorial-search/?search_foss=UCSF+Chimera&search_language=English

To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on UCSF Chimera interface.

Please refer to the link below for tutorials on UCSF Chimera series.

Slide number 7


Code Files

  • The input files required for this tutorial are available in the Code files link.
  • Please download and extract the files.
Slide number 8

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.
Double-Click on Chimera icon on the desktop. I will open the Chimera interface by double-clicking on the shortcut icon on my Desktop.


Chimera interface opens.

Click on the File menu on the main menu bar.

Select Open option.

From the Open file in the Chimera dialog-box, select 2vta.pdb option.

Let us load the structure of the receptor on the panel.

Click on the File menu on the main menu bar.

Select Open option.

Open file in Chimera dialog-box opens.

From the dialog-box, select 2vta.pdb option.

Click on the Open button at the bottom.

Cursor on the panel.

Click on the Presets menu.

Select Interactive 1 (ribbons) option.

The receptor-ligand complex loads on the panel.

For me the complex opened in ribbons display.

In your case, it may open in a different format.

You can change it to ribbons format using the Presets menu on the menu bar.

Select Interactive 1 (ribbons) option to change the display.

Cursor on the panel.

Cursor on the ligand.

CELL DIVISION PROTEIN KINASE 2, amino acids 298, chain A

Ligand is small molecule indazole

The receptor here is the cyclin dependent kinase inhibitor.

The ligand is an Indazole molecule.

Cursor on the ligand. We need to delete indazole, glycerol and water molecules from the structure.
Click on the Select menu, from the drop-down select Residues option.

Cursor on GOL, HOH and LZ1.

Click on Select menu, from the drop-down select Residue option.

The sub-menu shows 3 residues under the All nonstandard category.

GOL, HOH and LZ1, that is, glycerol, water and Indazole respectively.

Click on GOL. Each time I will select a residue, and delete it.

I will click on GOL which is glycerol.

Cursor on glycerol structure.

Click on the Actions menu, from the drop-down select Atoms/Bonds.

From the sub-menu select the delete option.

Cursor on the panel.

Glycerol molecules get highlighted on the panel in green color.

Click on the Actions menu, from the drop-down select Atoms/Bonds.

From the sub-menu select the delete option.

Glycerol molecules get deleted from the panel.

Click on the Select menu.

From the drop-down select Residues option choose HOH/LZ1.

Click on the Actions menu, from the drop-down select Atoms/Bonds.

From the sub-menu select the Delete option.

Let us delete water molecules and indazole ligand from the structure.

Select water molecules, they are highlighted in green color.

Delete the water molecules from the structure.

Similarly select indazole molecule and delete it.

Cursor on the panel. To this receptor structure we will add the best pose conformation of the ligand obtained by autodock runs.
Click on the File menu

select Open, Open file in Chimera.

dialog-box opens.

Click on the File menu and select Open, Open file in Chimera dialog-box opens.

Select ligand-conf1.pdb from the list.

In the File type field select PDB from the list.

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

From the File menu, select Open option.

Open file in Chimera dialog-box opens.

From the list of files select the pdb file containing the best pose of the ligand from the autodock runs.

We had saved this file earlier as ligand-conf1.pdb.


I will select the file from the list.

In the File type field select PDB from the list.

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

Cursor on the panel. On the panel you can see the best conformation of the indazole added to the receptor structure.
Slide Number 9

Chimera Tools for Visualization.

Using tools in Chimera we can visualize receptor-ligand interactions.

The two kinds of interactions,

  • hydrogen bonds and
  • other polar and non-polar interactions can be visualized.

We can also visualize the active site pocket and surface properties of the receptor.

Slide Number 10

Active Site Residues

Lys33, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Asp86, Leu134, and Asp145.

From the literature, the following residues form much of the ligand binding pocket:

Let us highlight these residues in the structure on the panel.

Cursor on the panel. Back to the Chimera interface.

We will use the command line to select and highlight the active site residues.

Click on the Favorites menu.

Select the Command Line option from the drop down.

Click on the Favorites menu.

Select the Command Line option from the drop down.

Cursor on the Command Line at the bottom of the interface. Command line panel opens at the bottom of the interface.

Here you can type the commands in the command field to modify the structure.

Type,

select :33.A

Press Enter.

Cursor on the panel.

Click on the Actions menu on the menu bar.

To select Lysine at position 33 on chain A, I will type , select space colon 33 dot A

Press Enter.

On the panel you can see the outline highlighted on the cartoon display.

We will display this amino acid as the ball and stick model.

Click on the Actions menu on the menu bar.

Select Atoms/Bonds, choose Show from the sub-menu. Select Atoms/Bonds, choose Show from the sub-menu.

Atoms are now displayed as sticks for the lysine.

Click on the Actions menu on the menu bar.

Select the Atoms/Bonds option.

Select Ball and stick from the menu.

Click on the Actions menu again and select the Atoms/Bonds option.

Select Ball and stick from the menu.

Lysine is now shown as a ball and stick display.

Actions menu again and select the colors option.

Select by element from the sub menu.

Click on the Actions menu again and select the color option.

Select by element from the sub menu.

On the panel you can see the ball and stick model in rasmol color coding of elements.

Click on Select option and clear the selection.

Type,

select: Amino acid code and position number (example Phe 80)

Press Enter.

Click on the Actions >> Atoms/Bonds >> Show

Actions >> Atoms/Bonds >> ball and stick

I will show the steps for one more AMINO ACID Phenylalanine 80.

At the command line edit the command as shown.

Delete the number 33.A

and in its place type 80.A, rest of the command remains as such.

Press Enter.

Phenylalanine 80 is highlighted. Phenylalanine 80 is highlighted.


Go to Actions menu and click on Show.

Phenylalanine 80 is shown in sticks display.


Go to Actions, Atoms/Bonds and click on ball & stick.

Go to Actions again select color by element.

Click on Select option and clear the selection.

Cursor on the panel. Following the same steps, show all the amino acids in the active-site.

Now receptor-ligand complex with the active site amino acids are shown in ball and stick display.

Click on the Select menu, choose Residue, from the sub menu choose LZ1.


Cursor on the panel.

To view hydrogen bonds formed by ligand and receptor, select the ligand.

Click on the Select menu,and choose Residue, from the sub menu choose LZ1.

On the panel, LZ1 is highlighted in green color.

Click on the Tools menu.

Select Structure Analysis.

From the sub-menu choose FindHBond option.

Click on the Tools menu.

Select Structure Analysis.

From the sub-menu choose FindHBond option.

H-Bond Parameter dialog-box opens.

Click on the check box against Label Hydrogen bond with distance.

Click on Only find H-bonds with at least one end selected.

Click on Write information to reply log.

Click on the OK button.

H-Bond Parameters dialog-box opens.

In the dialog box,

Fix the color of the hydrogen bond by clicking the colored box.

I will select yellow color.

Close the Color selection box.

Fix the line width to 3.0 for a thicker line.

  • Click on the check box against Label Hydrogen bond with distance.
  • Click on Only find H-bonds, with at least one end selected.


Uncheck any other check boxes if checked.

  • And click on Write in formation to reply log.

Click on Apply and OK buttons.

Cursor on the panel. Observe the panel.

Hydrogen bonds are shown as pseudo-bonds of specified color and line width.

Here we can see only two hydrogen bonds with indazole.

Click on the Favorites menu on the menu bar.

From the sub menu select Reply log option.

Details of the bonds can be viewed on the Reply log.

Open Reply log using Favorites menu.

Click on Favorites menu.

From the sub menu select Reply log option.

A pop-up window opens.

Information about each hydrogen bond is given here.

Cursor on the Reply log pop-up information.

Close the pop-up window.

One of the bonds, is formed with Leucine 83 and indazole nitrogen.

Another is formed with Glutamine 81 with hydrogen attached to the nitrogen atom of indazole.

Cursor on the panel. On the panel we can see the hydrogen bond distance.

Close the Reply log window.

Click on the Tools menu.

Select Structure Analysis from the sub-menu choose Findclashes/contacts option.

There is another feature in the Tools menu under the Structure Analysis option. 
It is Findclashes/contacts.

A dialog box opens.

This feature identifies non-polar interactions such as Clashes and Contacts.

Click on Designate in the Find Clashes/Contacts dialog box. Let us identify contacts of the LZ1 with all other atoms.

Ligand is already selected on the panel.

Click on Designate in the Find Clashes/Contacts dialog box.

It shows 10 atoms designated.


Click on the radio button against “All other atoms”.

Click on the radio button against “All other atoms”.


Point to Include intra-molecule contacts.

In the Clash/Contact Parameters section, in the Default click on the Contact button.
Under Treatment of Clash/Contact Atoms, click on the following check boxes.
  • Select
  • Draw pseudo-bonds
  • If endpoint atom hidden
  • And Write information to reply log
Under Treatment of Clash/Contact Atoms,

click on the following check boxes.

  • Select and
  • Draw pseudo-bonds of color.

Click on the color box.

In the Color Editor window I will select green.

Close the color selector.

Check the check box for, Write information to reply log.

Click on the OK button.

Cursor on the panel.

Click on the OK button.

Observe the panel.

All the contacts of ligand LZ1 are shown as green lines.

Click on the Favorites menu.

Select Reply Log from the sub-menu.

Cursor on the Reply Log window.

Open the Reply Log using the Favorites menu.

Atom-atom contacts are listed here.

It shows 21 contacts.

The amino acid residues which made the contact with LZ1 are listed here.

Close the dialog-box.

These residues form the binding site for this receptor-ligand complex.

Cursor on the panel. Most of these active site residues are hydrophobic in nature.


Let us create a surface for this complex colored by amino acid hydrophobicity.

Cursor on the panel. Using the Presets menu let us analyze the hydrophobic surface for this complex.
Click on Presets on the menu bar. From the drop down select Interactive 3 hydrophobicity surface. Click on Presets on the menu bar.

From the drop down select Interactive 3 hydrophobicity surface.

Cursor on the panel. The surface represents blue for the most polar residues,

orange for the most hydrophobic,

white for the neutral amino acids.

Cursor on the panel.

Rotate and zoom the structure using the mouse.

We will rotate and locate the ligand pocket.

As you notice here, most of the ligand binding pocket is hydrophobic.

Click on the Viewing Controls in the Tools menu.

Select Side View from the drop down.

The interior of the binding pocket can be viewed using the Viewing Controls in the Tools menu.

Select Side View from the drop down.

In the Viewing window,Check the check box for Clip at the bottom left.

Click on the Surface Capping button.

In the pop-up window, check the box for cap surfaces at clip planes and use cap color and cap style.

Click on the color box next to use cap color to select the color of the cap.

Click on Close button

A Viewing window opens.

You will see a viewing eye and two cutting planes in the Viewing window.

Check the check box for Clip at the bottom left.

Click on the Surface Capping button.

Surface Capping window opens.

Check the box for cap surfaces at clip planes and use cap color and cap style.


Click on the color box next to use cap color to select the color of the cap.

I will select pink.


Close the color editor.

I will select cap style as solid.


Click on Close button to close the surface capping window.

Change the position of the viewing eye and clipping planes. We can change the position of the viewing eye and clipping planes.

Now we can view the interior of the binding pocket clearly.

You can see clearly that the ligand is attached to the hydrophobic pocket.

Slide Number 11


Conclusion of the Analysis

Conclusion of the Analysis


The ligand is interacting mostly with the hydrophobic residues inside the binding pocket.

We found many non bonding interactions with the hydrophobic residues.

Slide Number 12


Conclusion of the Analysis

Only a few hydrogen bonds a re expected.

We observed only two hydrogen bonds using the Structure Analysis tool.

Cursor on the panel. More hydrophobic groups on the indazole will increase the interaction and binding with the active site.

We can generate and analyze more conformers to understand the interactions better.


This brings us to the end of this tutorial.

Slide Number 13

Summary

Let us summarize,

In this tutorial, we have,


Opened the PDB file for the receptor on the Chimera interface.


Selected and deleted solvent and other residues from the receptor structure.


Slide Number 14

Summary

Added the most preferred conformation of the ligand obtained after autodock runs to the receptor structure.


Showed hydrogen bonds and other interactions of the ligand with the receptor.

Slide Number 15

Summary

Highlighted the active site residues.


Showed the receptor-ligand surface and active site pocket.

Slide Number 16

Assignment

As an assignment,

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

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

Slide Number 17


About Spoken Tutorial Project

  • The video at the following link summarizes the Spoken Tutorial project.
  • Please download and watch it.
Slide Number 18


Spoken tutorial workshops

  • We conduct workshops using spoken tutorials and give certificates.
  • For more details, please write to us.
Slide Number 19


Forum

Please post your timed queries in this forum.
Slide Number 20


Acknowledgment

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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