View source for AutoDock4/C2/Visualizing-Docking-using-UCSF-Chimera/English



'''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.


{| border=1
|-
|| 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 A'''ll 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 no n-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'''

|| 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.

|-
|| 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 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.
|-
|}