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  • Assignment Molecular Docking Name: Matric No

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    elly loliey
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    This document contains instructions for a molecular docking assignment involving the COVID-19 main protease protein (PDB code 6LU7). Students are asked to 1) redock the original ligand N3 to validate the docking procedure, 2) dock a new ligand, remdesivir, to the protein, and 3) compare the binding energies of N3 and remdesivir to determine which binds more strongly and thus better inhibits the protease.

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    CHM3701 assignment 9

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    This document contains instructions for a molecular docking assignment involving the COVID-19 main protease protein (PDB code 6LU7). Students are asked to 1) redock the original ligand N3 to validate the docking procedure, 2) dock a new ligand, remdesivir, to the protein, and 3) compare the binding energies of N3 and remdesivir to determine which binds more strongly and thus better inhibits the protease.

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    15 views1 page

    Assignment Molecular Docking Name: Matric No

    Uploaded by

    elly loliey
    This document contains instructions for a molecular docking assignment involving the COVID-19 main protease protein (PDB code 6LU7). Students are asked to 1) redock the original ligand N3 to validate the docking procedure, 2) dock a new ligand, remdesivir, to the protein, and 3) compare the binding energies of N3 and remdesivir to determine which binds more strongly and thus better inhibits the protease.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
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    ASSIGNMENT MOLECULAR DOCKING

    Name:
    Matric No:

    Question 1: Redocking
    Download the protein structure (PDB code: 6LU7) from Protein Data Bank. Prepare the receptor and ligand (N3 which
    consists of: 02J1, ALA2, VAL3, LEU4, PJE5 and 0106) in pdbqt format. Run the molecular docking using AutoDock Vina.
    Give the binding energy result and the picture of complex (surface and stick representation).

    Question 2: New Ligand


    By using the same protein receptor, replace the ligand with the new ligand which is remdesivir. Download this ligand from
    PubChem Database and prepare the new ligand in pdbqt format. Run the molecular docking using AutoDock Vina. Give the
    binding energy result and the picture of complex (surface and stick representation).

    Question 3: Result Comparison


    Determine which ligand (N3 or remdesivir) is better for inhibiting COVID-19 main protease and explain why.

    Remdisivir is better for inhibiting COVID-19 main protease than N3 because it has high
    binding affinity compare to N3. The more negative the affinity value, the better the binding
    affinity.

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