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    Advance Pharmacology: Lab Worksheet: Practical 1

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    Wincent Huang
    Molecular docking is used to predict how molecules interact and bind to each other. It has applications in areas like drug discovery, bioremediation, and virtual screening. The document describes a lab worksheet on molecular docking that involves preparing receptor and ligand files, running docking simulations, and analyzing the results. The top ten docking poses are reported based on binding free energy scores, with the first pose having the lowest (best) score, indicating good binding between the ligand and receptor.

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    Advance Pharmacology: Lab Worksheet: Practical 1

    Uploaded by

    Wincent Huang
    50 views3 pages
    Molecular docking is used to predict how molecules interact and bind to each other. It has applications in areas like drug discovery, bioremediation, and virtual screening. The document describes a lab worksheet on molecular docking that involves preparing receptor and ligand files, running docking simulations, and analyzing the results. The top ten docking poses are reported based on binding free energy scores, with the first pose having the lowest (best) score, indicating good binding between the ligand and receptor.

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    ADV PHARMA PRAC 2 & 3

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    Molecular docking is used to predict how molecules interact and bind to each other. It has applications in areas like drug discovery, bioremediation, and virtual screening. The document describes a lab worksheet on molecular docking that involves preparing receptor and ligand files, running docking simulations, and analyzing the results. The top ten docking poses are reported based on binding free energy scores, with the first pose having the lowest (best) score, indicating good binding between the ligand and receptor.

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    Download as docx, pdf, or txt
    50 views3 pages

    Advance Pharmacology: Lab Worksheet: Practical 1

    Uploaded by

    Wincent Huang
    Molecular docking is used to predict how molecules interact and bind to each other. It has applications in areas like drug discovery, bioremediation, and virtual screening. The document describes a lab worksheet on molecular docking that involves preparing receptor and ligand files, running docking simulations, and analyzing the results. The top ten docking poses are reported based on binding free energy scores, with the first pose having the lowest (best) score, indicating good binding between the ligand and receptor.

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    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.

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