Difference between revisions of "AutoDock4/C2/Getting-Started-with-Docking/English"
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||Open the terminal using the show applications icon. | ||Open the terminal using the show applications icon. | ||
− | |||
||The next step is ligand refinement. | ||The next step is ligand refinement. | ||
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Type the system password. | Type the system password. | ||
− | ||I am using the Ubuntu 20.04 system | + | ||I am using the Ubuntu 20.04 system. |
+ | |||
+ | Hence I will click on the '''Show Applications''' button at the bottom-left. | ||
On the search bar that appears I will type '''Terminal'''. | On the search bar that appears I will type '''Terminal'''. | ||
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'''/home/snehalatha''' | '''/home/snehalatha''' | ||
− | || Click on | + | || Click on “'''Remind me later'''”. |
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− | Select the '''mol2''' file of the ligand | + | Select the '''mol2''' file of the ligand, '''2vta_D_LZ1.mol2''' |
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Read the message and note the information. | Read the message and note the information. | ||
− | Click on | + | Click on OK button. |
|- | |- | ||
|| Click on '''Edit''' menu, select '''Hydrogens''', then select '''Add''' option. | || Click on '''Edit''' menu, select '''Hydrogens''', then select '''Add''' option. | ||
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− | Leave all other settings as such and click on '''OK'''. | + | Leave all other settings as such and click on the '''OK'''. |
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Click on '''Input''' then click on '''Open'''. | Click on '''Input''' then click on '''Open'''. | ||
− | Since we already saved the working directory, it is the default directory now. | + | Since we have already saved the working directory, it is the default directory now. |
|- | |- |
Revision as of 17:11, 23 October 2023
Title of script: Getting Started with Docking
Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar.
Keywords: autodock4, adt, mgl tools, ligand, receptor, rcsb protein data bank, ligand refinement, add hydrogens, detect root, rotatable bonds, pdb file, pdbqt file, video tutorial.
Visual Cue | Narration |
Slide Number 1
Title Slide |
Welcome to this tutorial on Getting Started with Docking. |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn to
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Slide Number 3
System Requirement |
Here I am using,
Ubuntu Linux OS version 20.04 AutoDockTools version 1.5.7 Google Chrome browser version 96.0.4 And a working internet connection |
Slide Number 4
Pre-requisites |
To follow this tutorial learner should be familiar with,
basic computer operations, and basic bioinformatics |
Open web browser, in the address bar type, 'rcsb.org
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Open any web browser.
We will now download the ligand and receptor files from Protein Data Bank.
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https://www.rcsb.org/structure/2VTA
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In the search field at the top, type the 4 letter PDB code 2VTA.
The page refreshes with the 3D model and information about the protein.
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Cursor on the blue Download Files button.
Click the Download Files button and select PDB format.
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On the right-side of the page, you will see a Download Files button.
From the drop down options select PDB format. |
Show the pdb file, 2vta.pdb in the Downloads folder. | The PDB file 2vta.pdb for the protein 2VTA downloads to your Downloads folder. |
Scroll down the page,
Choose MOL2 format, Chain D. |
Scroll down the page, in the Small Molecules section under Ligands ID you will see LZ1.
From the options in the drop down, choose MOL2 format, Chain D. |
Show the mol file 2vta_D_LZ1.mol2 | The mol file for the ligand downloads to the Downloads directory in my system.
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Click on the files 2vta.pdb and 2vta_D_LZ1.mol2.
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I will move both the downloaded files to my home directory.
From the options choose Move to option.
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Open the terminal using the show applications icon. | The next step is ligand refinement.
Open AutoDockTools also called ADT .
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At the terminal prompt type adt and press Enter.
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I am using the Ubuntu 20.04 system.
Hence I will click on the Show Applications button at the bottom-left. On the search bar that appears I will type Terminal. Then click on the terminal option on the screen. The terminal opens. At the prompt I will type adt and press Enter.
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Cursor on ADT interface.
Click on File >> Preferences >> Set.
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Click on “Remind me later”.
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Click on the Ligand tab on the menu bar (last row in the menu bar)
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To refine the ligand, click on Ligand tab on the menu bar.
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In the Ligand file for AutoDock4 , open 2vta_D_LZ1.mol2 file.
Click on the Open button at the bottom-right. |
The Ligand file for AutoDock4 dialog box opens.
So select Files of Type as Mol2 files from the drop-down.
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Cursor on the display panel.
Cursor on the pop-up window. Click on OK. |
The structure will appear in the display panel on the ADT interface.
Click on OK button. |
Click on Edit menu, select Hydrogens, then select Add option.
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Since this structure was derived from the protein data bank, it does not contain hydrogens.
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Slide Number 5
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This step can be ignored in cases where the ligand structure is generated by other means such as:
quantum mechanical optimization or draw the 2D structure and convert to 3D in Open Babel.
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Go to File menu, >> Save >> Write PDB.
Type the file name as Ligand.pdb Cursor on Browse button. Click OK to close the dialog box. |
Now we have to save this structure in pdb format.
From the sub-menu select Write PDB.
|
Cursor on ADT interface. | Now we need to prepare the ligand for docking. |
Close the window by File >> Exit
In the Quit dialog box, Do you wish to Quit? click on OK. |
Let us close the existing ADT window.
Go to File menu and click on Exit option.
click on OK button. |
At the terminal prompt type adt and press Enter. | To open a new ADT interface use the terminal as we did before.
ADT window opens. |
Go to Ligands menu >> Input >> Open. | Go to Ligands menu.
Click on Input then click on Open. Since we have already saved the working directory, it is the default directory now. |
Select Files of Type as PDB files from the drop-down.
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Select Files of Type as PDB files from the drop-down.
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Cursor on the adt display panel. | The structure will appear in the display panel of ADT.
Read the message and click Ok to continue. |
Click Ligand >> Torsion Tree >> Detect Root.
Cursor on the green sphere on nitrogen atom. |
Click Ligand and select Torsion Tree then choose Detect Root.
A green sphere will appear over the indazole Nitrogen atom.
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Click Ligand >> Torsion Tree >> Choose Torsions.
Cursor on Torsion Count dialog box.
Click Done to close the window. |
To visualize which bonds are allowed to be rotatable,
Torsion Count dialog box opens. This will change the color of all the bonds to demonstrate which are rotatable.
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Click Ligand >> Output >> Save as PDBQT.
A dialog box opens, file name is auto populated as ligand.pdbqt. Click on Save button. |
Save the file as a .pdbqt file.
Then select Save as PDBQT.
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Slide Number 6
Summary slide |
Let us summarize,
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Slide Number 7
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As an assignment
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Slide Number 8
About Spoken Tutorial Project |
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Slide Number 9
Spoken tutorial workshops |
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Slide Number 10
Answers for THIS Spoken Tutorial |
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Slide 11
Acknowledgement |
Spoken Tutorial project was established by 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. |