Difference between revisions of "Molecular and Homology Modeling project"

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= Molecular Modelling =
= Molecular Modelling =


* Rendering a Protein with PyMOL
* [https://hygieia.rx.uga.edu/labwiki/index.php/PHRM_8010_Lead_Drug_Discovery_Molecular_Modelling-PyMOL_Tutorial Learn how to render a protein with PyMOL]<ref name=":0">You will need the password for the labwiki.org website to access this.</ref>
* Instructions on drawing a small molecule with Avogadro
**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.
**# '''4 points:''' Publication quality figure, showing secondary structure of your protein saved as a png file and a pse file.
**# '''4 points:''' B-factor coloring your your protein saved as a png file and pse file.
**# '''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 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.
**# '''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 [https://hygieia.rx.uga.edu/labwiki/index.php/PHRM_8010_Lead_Drug_Discovery_Molecular_Modelling-Avogadro_Tutorial instructions on drawing a small molecule with Avogadro]<ref name=":0" /> below.
** 20/50 points
** Files that need to be created for the project.
**# '''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.
**# '''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.
**# '''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.
**# '''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.
**# Send all the files to me in a single compressed folder by email.
 
= Molecular Docking =
 
* 10/50 points
*Pick one option:
*# If you have a small molecule drug for your Capstone Presentation, dock your small molecule with [http://www.swissdock.ch/ SwissDock.]
*#*Use the biological target of your Capstone Presentation for the biological target of  [http://www.swissdock.ch/ SwissDock.]
*# If you have a biologic drug for your Capstone Presentation, dock your biologic with [https://cluspro.org/login.php ClusPro].
*#*Use the biological target of your Capstone Presentation for the biological target of [https://cluspro.org/login.php ClusPro].
*Send me the graphical and text output of the molecular docking that you did with [http://www.swissdock.ch/ SwissDock] or [https://cluspro.org/login.php ClusPro].
 
= Homology Modelling =
 
* Since we never talked about it, this part will be cancelled.
 
= References and Notes =

Latest revision as of 15:51, 3 April 2022

Molecular Modelling

  • Learn how to render a protein with PyMOL[1]
    • 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[1] 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.

References and Notes

  1. 1.0 1.1 You will need the password for the labwiki.org website to access this.