View source for Molecular and Homology Modeling project

= Molecular Modelling =

* [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>
**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 =