Module 3 Protein & Ligand Preparation

 

Module 3 – Protein & Ligand Preparation in clear step-by-step activity format, continuing from where Module 2 left off.
We’ll still use ACE (1O8A) as the example protein and Lisinopril as the ligand for hypertension drug discovery.

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Module 3: Protein & Ligand Preparation for Docking

Objective:
Prepare both the protein (target) and ligand (drug molecule) files in the correct format for AutoDock Vina.

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Step 1 – Clean the Protein Structure

1. Open protein file (1O8A.pdb) in PyMOL or UCSF Chimera.

2. Remove water molecules:

   • In PyMOL:

     arduino
     remove solvent
     

   • In Chimera:
     Select → Structure → solvent → delete.

3. Remove any ligands or ions from the protein that are not needed for docking.

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Step 2 – Save Clean Protein File

1. After removing unwanted molecules,
   save as ACE_clean.pdb.

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Step 3 – Add Hydrogens & Charges to Protein

1. Open AutoDockTools (ADT).

2. Load protein → ACE_clean.pdb.

3. Add polar hydrogens:
   Edit → Hydrogens → Add → Polar only.

4. Add Gasteiger charges:
   Edit → Charges → Compute Gasteiger.

5. Save as ACE_clean.pdbqt.

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Step 4 – Prepare Ligand

1. Download Lisinopril from PubChem in .SDF format.

2. Convert .SDF → .PDB using OpenBabel:

   bash
   obabel lisinopril.sdf -O lisinopril.pdb
   

3. Open ligand in AutoDockTools.

4. Add hydrogens and Gasteiger charges.

5. Save as lisinopril.pdbqt.

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Step 5 – Define Docking Grid Box

1. In AutoDockTools, load both protein (ACE_clean.pdbqt) and ligand (lisinopril.pdbqt).

2. Select binding site region (around active site residues).

3. Set grid box center coordinates (X, Y, Z).

4. Set box size to cover the active site completely.

5. Save grid configuration as conf.txt.

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Step 6 – Verify Files

• Protein → ACE_clean.pdbqt

• Ligand → lisinopril.pdbqt

• Config file → conf.txt
  All ready for docking in Module 4.