#2 Activity

 Here’s a step-by-step activity list for Module 2 – Installation & Environment Setup (with AutoDock & Python tools) in your drug discovery workshop, using a real-life example file:

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Activity: Installing Tools & Preparing the Environment for Hypertension Drug Discovery

Objective:

Get participants ready to perform molecular docking using AutoDock with a real hypertension-related protein (ACE – Angiotensin-Converting Enzyme).

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Step 1 – Download & Install Python

1. Visit https://www.python.org/downloads/

2. Download Python 3.11+ (Windows/Mac/Linux).

3. During installation, check "Add Python to PATH".

4. Verify installation in terminal:

   python --version
   

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Step 2 – Install Required Python Libraries

1. Open Command Prompt / Terminal.

2. Install required packages:

   pip install numpy pandas biopython matplotlib vina
   

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Step 3 – Download & Install AutoDock Vina

1. Go to https://vina.scripps.edu/downloads/

2. Select your OS version (Windows/Mac/Linux).

3. Extract files to a known folder (e.g., C:\AutoDockVina).

4. Add the folder to PATH in system environment variables.

5. Test installation:

   vina --help
   

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Step 4 – Download a Real-Life Protein Example (ACE)

1. Open RCSB PDB: https://www.rcsb.org/

2. Search for ACE protein (PDB ID: 1O8A as example).

3. Download PDB file to your working directory.

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Step 5 – Install Visualization Tool (PyMOL or UCSF Chimera)

1. Download PyMOL (open-source): https://pymol.org/2/

2. Install it and verify by opening 1O8A.pdb from Step 4.

3. Rotate and zoom to observe protein structure.

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Step 6 – Prepare Ligand File

1. Download a known hypertension drug structure (e.g., Lisinopril) from PubChem: https://pubchem.ncbi.nlm.nih.gov/.

2. Save in SDF format.

3. Convert to PDBQT format using OpenBabel:

   obabel lisinopril.sdf -O lisinopril.pdbqt
   

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Step 7 – Check Everything Works

1. Open 1O8A.pdb in PyMOL.

2. Load lisinopril.pdbqt in Vina.

3. Run a test docking to confirm setup.

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