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Institutional Summer Training Worksheet

The document provides steps for performing site specific molecular docking of a ligand to a protein using Discovery Studio and AutoDock tools. Key steps include: 1. Preparing the protein file by removing water molecules and existing ligands from the binding site. 2. Setting up the docking parameters like defining the binding site and adding charges to the protein and ligand files. 3. Running the docking simulation to generate output files containing docked poses and binding affinities. 4. Analyzing the docked poses and interactions between protein and ligands using Discovery Studio.

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Apoorva Singh
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0% found this document useful (0 votes)
49 views9 pages

Institutional Summer Training Worksheet

The document provides steps for performing site specific molecular docking of a ligand to a protein using Discovery Studio and AutoDock tools. Key steps include: 1. Preparing the protein file by removing water molecules and existing ligands from the binding site. 2. Setting up the docking parameters like defining the binding site and adding charges to the protein and ligand files. 3. Running the docking simulation to generate output files containing docked poses and binding affinities. 4. Analyzing the docked poses and interactions between protein and ligands using Discovery Studio.

Uploaded by

Apoorva Singh
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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INSTITUTIONAL SUMMER TRAINING

Worksheet
Name: Apoorva singh UID: 20BBE1018
Branch: B.E. Biotechnology Section/group: B
Semester: 3rd Subject code: 20BEY-211
For site specific molecular docking, protein chosen is: 4OVZ
Steps to prepare protein:
 Open DISCOVERY STUDIO VISUALIZER.
 Click on FILES, choose ‘ OPEN’, then choose your protein file.

 Click on ‘VIEW’ , and hit HIERARCHY, a protein tray will appear


which is very useful in protein preparation.
 Select water molecules and hit DELETE.(basically we have to
remove the water molecule so that it do not interfere with the
binding site)
 Now from protein tray, choose ligand 1, click on define and
edit binding and hit from current selection.
 A red circle will appear, which will cover the ligand.
 Now, this is actually the place where we need to dock our
ligand. So, we will remove the ligand from here and will dock
our ligand ( taken from zinc database) here.
 Click on sbd_site_sphere to increase the sphere size.

 Ligand 1, ligand 2 and ligand 3 are under this sphere now.


 Now we have to remove these ligands, so hit sbd_site_sphere,
click on attributes of sbd_site_sphere, choose xyz coordinates
and apply in grid configuration.
 From protein tray, click on ligand groups, click edit and hit
delete.
 Delete chain B.
 Go on to Chemistry, click on Hydrogen and hit polar only.
 Save this in pdb format. (Protein.pdb)
NOW:
 Open AUTODOCK.
 Open you prepared protein file (Protein.pdb)

 Check the chain ( it will only have chain A).


 Go onto edit, add Kollman charges.
 Click on edit and compute Gasteiger charges.
 Click on atoms and assign AD4 type.
 Now save it in pdbqt format. (Protein.pdbqt)
 While saving, a box will appear, from that, click on atom, press
shift and click end. Hit add.
Steps to prepare ligand:
 Click on Ligand  Input  Open .
 Choose ligand.pdb file.
 Now click on Torsion tree, then click on Choose root.
 Then again, Torsion tree then detect root.

 Save the ligand in pdbqt form. (Ligand.pdbqt)


NOW:
 Click on grid then click on choose and from the box (that
appears), hit Protein.
 Now, set map type select Ligand.
 Prepare a configuration file. (receptor file)
 After preparing configuration file and saving it in docking
folder, open Command prompt.
 Now copy the location of your docking folder and paste it in
command prompt. ( so that it can read all the necessary
files)
 Press enter.
 Now type “vina.exe --config confi.txt --log log.txt” , after
this press enter and wait for some time now.
 The program is running and is analysing the binding site.
 Result is executed. Output file is ready (it is in pdbqt format).
 Binding affinity has appeared.

 Now, split the output file.


 For splitting, type “vina_split.exe –input out.pdbqt” (out.pdbqt
is the output file that was generated).

Now for analysing the result, open BIOVIR DISCOVERY STUDIO:


 Go to file  open  choose protein.
 Now, choose all the 9 ligands.
 All the 9 ligands will open in separate windows.
 Copy out ligand 1  choose protein  go to view and hit
hierarchy. Paste the copied out ligand 1 there.
 Repeat the above step for all the out ligands.
 Now we will be able to see pose of all the ligands in the
structure.

 · After this if we want to analyze a specific ligand, we will


remove the tick from all the others. That specific ligand will
now be visible with structure.
 · Now in order to analyze the interaction diagram, we will click
on view interactions  select the ligand for analysis. After this,
click on ligand interaction and now we will be able to see the
ligand interaction.
 · Now if we want to see the data table, we will click on view ->
data table. The data table will be displayed at the bottom side.
This data table provides us the information about all the
interactions.

 · Now to see these interactions in 2D diagram, we will click on


show 2D diagram. An image will be displayed showing 2-D
interactions.

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