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Igem Docking13

The document outlines a practical exercise in pharmacoinformatics focused on virtual screening using the iGEMDOCK tool. It details the methodology for creating folders, downloading PDB complexes, generating derivatives of fluorouracil, and performing docking and interaction analysis. The conclusion highlights the successful virtual screening and analysis of compounds, including their binding affinities and interactions with the receptor.

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Madhur Miradwal
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32 views8 pages

Igem Docking13

The document outlines a practical exercise in pharmacoinformatics focused on virtual screening using the iGEMDOCK tool. It details the methodology for creating folders, downloading PDB complexes, generating derivatives of fluorouracil, and performing docking and interaction analysis. The conclusion highlights the successful virtual screening and analysis of compounds, including their binding affinities and interactions with the receptor.

Uploaded by

Madhur Miradwal
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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Pharmacoinformatics Date of Performance: 09-08-2024

Practical no: 6
Aim: To perform Virtual Screening using iGEMDOCK.

Theory:

iGEMDOCK is a comprehensive and easy-to-use tool that supports both virtual


screening and post-screening analysis for drug discovery. It provides an integrated
environment with two main features: docking/screening tags that focus on predicting
how chemical molecules bind to known 3D protein structures, and post-analysis tags
that provide detailed analysis of protein-ligand and connectivity properties of docked
poses.

Methodology:

❖ Create Folders:

• Create a folder on the desktop and name it as "virtual screen."


• Go to the menu and create a folder in the C drive under "igm doc" and name it
"VS_madhur."
• Inside the "VS_madhur" folder, create three sub-folders named "ligand," "receptor," and
"output."

❖ Download PDB Complex:

• Download the PDB complex for fluorouracil from the RCSB website.
• Note down the ligand number for fluorouracil.
• Place the downloaded file into the "receptor" folder.

❖ Obtain Canonical SMILES:

• Go to the Pumpkin database and search for the drug fluorouracil.


• Open the first search result.
• Copy the canonical SMILES of fluorouracil.

❖ Use ChemSketch:

• In the menu, search for "ChemSketch."


• Open ChemSketch and begin sketching.
• Go to the tools section, select "Generate Structure from SMILES," and paste the canonical
SMILES. Press OK.
• Clean the structure using the scissor symbol.
• Go to "File" in the top-left corner and save it in "2000 mol format."
• Name the file "floro-original" and save it on the desktop.

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Pharmacoinformatics Date of Performance: 09-08-2024

❖ Create Derivatives:

• Start creating 5 derivatives from the original fluorouracil drug.


• Open the "floro_original" file and add an oxygen atom. Clean the structure and save it as
"fluoro_D1" in the desktop folder.
• Repeat the same process for the other derivatives (D2, D3, D4, D5), adding different
functional groups.

❖ Process Derivatives in ArgusLab:

• Open ArgusLab, go to "File" and select the derivative "fluoro_D1."


• Clean the geometry, save the compound, and close the program.
• Repeat the same process for the rest of the derivatives (D2, D3, D4, D5).

❖ Save Compounds:

• Copy all six compounds (in PDF format) obtained from ArgusLab.
• Paste them into the "ligand" folder inside the "igm doc" folder.

❖ Configure Binding Site:

• Go to the "igm doc" folder in the C drive, then open the "bin" option.
• A grey-colored dialog box will appear.
• Set the output path by clicking on the output path option.
• Navigate to the "VS_gauri" folder and select it.
• Go to the "prepare binding site" option and select the "Display" option on the right side.
• Choose the binding option and check if the small arrow-shaped drop-down shows "URF,"
which should match the ligand name from the PDB website.
• Click "Observe."

❖ Modify Binding Site Background:

• In the command line window, enter background white and close the window.
• Return to the "prepare binding site" option.
• If the "Armstrong" option is checked, uncheck it.
• Click "Observe" again.
• In the command line, enter background purple or background white to change the
background color as desired.
• Close the window.

❖ Prepare Compounds for Docking:

• In the main dialog box, click on "Prepare Compounds."


• Select all compounds and delete them from the list.
• Add ligands from the top-left corner where the PDB files are listed and select all of them.
• Ensure the default setting is "Drug Screening."
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Pharmacoinformatics Date of Performance: 09-08-2024

• Click "Start Docking." (Note: This will result in an error after a few minutes.)

❖ Use UCSF Chimera:

• Go to the menu and search for UCSF Chimera.


• Head to the "Tools" section and go into the ligand folder. Copy the ligand path.
• In Chimera, go to "File," then "Open," and paste the ligand path into the dialog box that
appears. Press Enter.
• You will see molecules D1, D2, D3, D4, and D5.
• Click on molecule D1 and open it. A black background will appear.
• Go to "File" on the left, click "Save PDB," and save it in the folder "VS_madhur."
• Ensure the ligand name matches (e.g., "fluoro_D1"), then click "OK" and confirm the
overwrite by selecting "Yes."

❖ Analyze Interaction:

• A dialog box will appear in "igm doc."


• Select the small diamond-shaped option in the square and click "Display."
• You will see one or more molecules.
• At the top-right corner, click on "Interaction Analysis" to view the table.
• To check residues, click on "Residues" and save all the residue data.
• In the display option, head to "Display Treeview." A treeview table will be displayed
showing the black-colored residues and green-colored interactions.

❖ Save Results:

• Save the analysis in an Excel file in the output folder and name it "T1.xls."
• To get the summary table, save all of the files in the folder as text files.

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Pharmacoinformatics Date of Performance: 09-08-2024

Results:

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Pharmacoinformatics Date of Performance: 09-08-2024

Fig:- Fluorouracil Chemskech

D1 D3 D5

Fig: Argus lab

Fig: Rasmol

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Pharmacoinformatics Date of Performance: 09-08-2024

Fig : Chimera

Fig : Igem Docking completed

Fig : Interaction Analysis

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Pharmacoinformatics Date of Performance: 09-08-2024

Fig : Tree table view

Fig : Fitness table


Interpretition : It reflects the predicted binding affinity of the ligand to the receptor. Lower
fitness scores usually indicate better binding affinity, meaning the ligand fits better into the
receptor's binding site.

Fig : Interaction table

Interpretation:

Provides a detailed breakdown of the interactions between the ligand and the receptor,including the
fitness score as well as the interaction analysis with different amino acids.

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Pharmacoinformatics Date of Performance: 09-08-2024

Conclusion:

Using the iGEMDOCK tool, a virtual screening of receptors, and 5 derivatives was performed.

After docking the proteins, post-docking screen analysis was performed. Here, compounds along

with their energy, H-Bonds, etc. were found.

DY22SBBUOBID013

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