Pharm 8010 Assignments

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Assignment #6- Molecular Modeling

  • Small Molecule Modeling (20 points; 4 points for each)
    1. Download and install Avogadro
    2. Building molecules using what you learned in these tutorials.
      • You will need to get the login and password from me.
    3. (4 points) Download a small molecule from PubChem that begins with the first letter of your name and save it in png image format in Avogadro.
      • Everyone in the class should have a different small molecule even if your first names have the same first letter.
    4. (4 points) Download a small molecule from PDBeChem that is found in the protein that you chose as part of Molecule Modeling I and save it in png image format in Avogadro. If your protein doesn't have a small molecule associated with it, pick a different one.
    5. (4 points) Download a small molecule from the ZINC Database using the Search-->Structure Feature and save it in png image format in Avogadro.
      1. The small molecule must have more than 10 carbons and be different than your fellow graduate students.
    6. (4 points) Build a hypothetical molecule (i.e. doesn't exist) of your choice in Avogadro and save it in the PDB format and export it into the png graphics format
      • Everyone should have a different small molecule. Use your imagination. It should be larger than acetaminophen. It should be more complex than a benzene ring. It can contain benzene rings.
      • The geometry of your small molecule needs to be energy minimized. Do not send me a molecule with extreme bond lengths and angles. Otherwise, you might lose a lot of credit
  • Protein Molecular Modeling (30 points; 10 points for each UCSF Chimera tutorial completed)

Old Version of the UCSF Chimera tutorial