Molecular and Homology Modeling project

Molecular Modelling

• Learn how to render a protein with PyMOL
  • 20/50 points
  • Analyze the boilogical target of your Capstone project, using techniques from the Molecular Modeling I tutorial on acylphosphatases, put not the protein from the tutorial
    • Recommendation: Do the PyMOL tutorial on acylphosphatases first before attempting your protein.
  • Files that need to be created for the project.
    1. 4 points: Publication quality figure, showing secondary structure of your protein saved as a png file and a pse file.
    2. 4 points: B-factor coloring your your protein saved as a png file and pse file.
    3. 4 points: Electron density around some part of your protein as a png and pse file.
       • Yu only need to pick one of the contour levels and either the 2FOFC or FOFC. In the tutorial, we do three different variations of the electron density map.
    4. 4 points: Electrostatic surface potential of your protein saved as a png file.
       • There may be some issues with the software, so you can get bonus points for doing this with your protein.
    5. 4 points: Movie of your protein in mpeg format
  • Send all the files to me in a zip single compressed folder by email.
• Regardless of whether your Capstone drug is a small molecule or biologic, please follow the instructions on drawing a small molecule with Avogadro below.
  • 20/50 points
  • Files that need to be created for the project.
    1. 5 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.
    2. 5 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.
    3. 5 points: Download a small molecule from the ZINC Database using the Search-->Structure Feature and save it in png image format in Avogadro.
       • The small molecule must have more than 10 carbons and be different than your fellow graduate students.
    4. 5 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.
    5. Send all the files to me in a single compressed folder by email.

Molecular Docking

• 10/50 points
• Pick one option:
  1. If you have a small molecule drug for your Capstone Presentation, dock your small molecule with SwissDock.
     • Use the biological target of your Capstone Presentation for the biological target of SwissDock.
  2. If you have a biologic drug for your Capstone Presentation, dock your biologic with ClusPro.
     • Use the biological target of your Capstone Presentation for the biological target of ClusPro.
• Send me the graphical and text output of the molecular docking that you did with SwissDock or ClusPro.

Homology Modelling

• Since we never talked about it, this part will be cancelled.