Advance Pharmacology: Lab Worksheet

Practical 1
1. What are the applications of Molecular docking? (3m)

Molecular docking is used in bioremediation to predict pollutants from soil, water and other
environments. It is also used in drug discovery such as discovering the binding site for drugs treating
AIDS. Lastly, molecular docking is applied in hit identification thought virtual screening.

2. State one difference between pdb and pdbqt file? (2m)

PDB format files do not include partial changes, white PDBQT format files does.

3. How many sub chains can be found in the receptors? (1m)

8 sub-chains.

4. Explain why we need to add hydrogen in ligand? (1m)

Because most macromolecular structure data do not contain hydrogen atoms in their PDB files.

5. Why we need to remove water molecule from the ligand? (3m)

Water molecules are not involved in the binding most of the time. Thus, they are removed to make
computations easier and water molecules might also distort the pose search is the binding pocket is
not being cleared.
Practical 2
1. Describe the different interactions between ligand and receptor? (4m)

Electrostatic forces : arise due to the presence of charge.

Electrodynamic forces : Van der Waals’ interactions are the most common type.

Steric forces : generated due to close proximity of molecules and affect the reactivity and the chemical
reactivity.

Solvent-related forces : the outcome of a chemical reaction between solvent and ligand.

2. What is conformational clustering histogram and free binding energy? (4m)

Conformational clustering sorts the docking results into conformationally similar bins, according to
the RMSD tolerance that is being set using the rmstol keyword. Free binding energy is a measurement
of the amount of energy available for the ligand to bind to the to the macromolecules in an isothermal
and isobaric thermodynamic system.

3. Copy and paste the top ten results obtained the end of the practical into the

worksheet. Explain the results.

Rank | Sub- | Run | Binding | Cluster | Reference | Grep

| Rank | | Energy | RMSD | RMSD | Pattern

_____|______|______|___________|_________|_________________|___________

1 1 17 -4.66 0.00 2.37 RANKING

1 2 11 -4.66 0.02 2.37 RANKING

1 3 8 -4.66 0.05 2.37 RANKING

1 4 19 -4.65 0.02 2.37 RANKING

1 5 6 -4.65 0.02 2.37 RANKING

1 6 9 -4.65 0.06 2.37 RANKING

1 7 14 -4.65 0.03 2.37 RANKING

1 8 16 -4.65 0.05 2.37 RANKING

1 9 12 -4.65 0.02 2.37 RANKING

1 10 18 -4.65 0.06 2.37 RANKING

The result shows the lowest to highest free energy binding.

4. What is Lamarckian GA? (1m)

A set of docking algorithms.

5. Can you tell from the results whether the ligand binds well to the receptor? Explain

your reasons. (2m)

Yes, because the free energy binding of the first result is the lowest compared to the other results.