Difference between revisions of "PHRM 8010"

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= Lectures =
= Computer Programming =
*[[Python Programming]]


* These are links that are specifically on the Wiki site. If a link is not present check ELC new.
= Dr. Roberts' Assignments =


{| class="wikitable"
* These are assignments that Dr. Roberts is responsible for. This does not apply to other lecturers in the course.
|+
'''Assignment #1:''' [https://hygieia.rx.uga.edu/pharmwiki/index.php/Graphing_and_Data_Analysis Graphing and Data Analysis]
!Date
!Title
!Link
|-
|
|'''Lecture 1'''
|
|-
|January 11, 2022
|Lead discovery and binding fundamentals
|
|-
|
|Presentation rubrics discussion with examples
|
|-
|
|Capstone Project Example: Basics of the Immune System
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|-
|
|'''Lecture 2'''
|
|-
|January 13, 2022
|Drug targets and epigenetics
|
|-
|
|Installation and introduction to Python programming
|[https://www.w3schools.com/python/default.asp Link]
|-
|
|Students select assignments and literature discussion
|
|-
|
|'''Lecture 3'''
|
|-
|
|
|
|}


= General =
* You can do the project that is explained or something more detailed.
* [[Pharm 8010 Assignments]]
 
* [[Python Programming]]
'''Assignment #2:''' [[NMR Spectrometer Simulator]] (10 out of 50 points)
**Chemoinformatics
 
***[https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_Pybel.html Pybel Module Tutorial]
* Dr. Zheng's part on organic chemistry = 25 points
***[https://rdkit.readthedocs.io/en/latest/GettingStartedInPython.html Rdkit Module Tutorial]
* Dr. Bartlett's part on M.S. spectrometry = 15 points
***[https://towardsdatascience.com/introduction-to-cheminformatics-7241de2fe5a8 Introduction to Cheminformatics]
* Dr. Robert's part with the NMR spectrometer simulator = 10 points
***[http://www.rdkit.org/docs/Cookbook.html Chemoinformatic Exercises in Python]
 
*[[R Programming]]
'''Assignment #3''': [https://hygieia.rx.uga.edu/pharmwiki/index.php/Bioinformatics_and_Chemoinformatics Bioinformatics and Chemoinformatics]
**Chemoinformatics
 
***[http://girke.bioinformatics.ucr.edu/manuals/vignettes/ChemmineR/ChemmineR.html#five-minute-tutorial Chemoinformatics tutorial in R]
* Requires installation of the Jupyter Lab IDE in Anaconda with Python version 3.7.1.1
*Recommend setting up a separate environment for doing this assignment
*If you have a small molecule drug for your Capstone project, pick three different methods to analyze your small molecule drug.
*If you have a biologic drug for your Capstone project, pick three different methods to analyze your small drug.
'''Assignment #4: Biologics-related presentation and discussion'''
 
* Dr. Kennedy's assignment.
 
'''Assignment #5: Essay on a newly developed biologic'''
 
* Dr. Kennedy's assignment.:
 
'''Assignment #6:''' [[Molecular and Homology Modeling project]]
 
* You can do this project on your drug and your biological target.
*Since we never talked about homology modelling, it has been cancelled as part of the assignment.
 
= NMR Challenge =
 
# [[Tutorials for the NMR challenge]].
# [https://hygieia.rx.uga.edu/labwiki/index.php/Pharm_8010_Processing_and_Analyzing_Protein_and_Small_Molecule_Data#Small_Molecule Small molecule NMR analysis of progesterone].<ref name=":0">You will need the password for the labwiki.org website to access this.</ref>
# [https://hygieia.rx.uga.edu/labwiki/index.php/Pharm_8010_Processing_and_Analyzing_Protein_and_Small_Molecule_Data#Protein Small molecule NMR analysis of ubiquitin.]<ref name=":0" />
 
= Capstone Presentation- Drugs and Targets =
* [https://hygieia.rx.uga.edu/pharmwiki/index.php/Table_of_Drugs_and_Targets Table of Drugs and Targets]
**You will have to pick a drug and a target. Each person will have a unique one. Please email it to me.
 
* [[Possible Outline for the Capstone Presentation]]
** When possible, you can use your drug (small molecule or biologic) and your biological target for the assignments.
 
= Potentially Useful Information =
 
*I have had native speakers in Chinese (several) and Italian attest to the accuracy of [https://www.deepl.com/translator DeepL Translate] to translate English into their native languages.
* I have had a native speaker attest to the accuracy of [https://translate.yandex.com/ Yandex] to translate English into Arabic.
*For speaking text in various languages, [https://aws.amazon.com/polly/ AWS Polly] seems to be the best.
*[[Chemical Class versus a Drug Class]]
 
= Old =
 
* [[Old Version of PHRM 8010 website]]
 
= References and Notes =
<references />

Latest revision as of 15:58, 20 April 2022

Computer Programming

Dr. Roberts' Assignments

  • These are assignments that Dr. Roberts is responsible for. This does not apply to other lecturers in the course.

Assignment #1: Graphing and Data Analysis

  • You can do the project that is explained or something more detailed.

Assignment #2: NMR Spectrometer Simulator (10 out of 50 points)

  • Dr. Zheng's part on organic chemistry = 25 points
  • Dr. Bartlett's part on M.S. spectrometry = 15 points
  • Dr. Robert's part with the NMR spectrometer simulator = 10 points

Assignment #3: Bioinformatics and Chemoinformatics

  • Requires installation of the Jupyter Lab IDE in Anaconda with Python version 3.7.1.1
  • Recommend setting up a separate environment for doing this assignment
  • If you have a small molecule drug for your Capstone project, pick three different methods to analyze your small molecule drug.
  • If you have a biologic drug for your Capstone project, pick three different methods to analyze your small drug.

Assignment #4: Biologics-related presentation and discussion

  • Dr. Kennedy's assignment.

Assignment #5: Essay on a newly developed biologic

  • Dr. Kennedy's assignment.:

Assignment #6: Molecular and Homology Modeling project

  • You can do this project on your drug and your biological target.
  • Since we never talked about homology modelling, it has been cancelled as part of the assignment.

NMR Challenge

  1. Tutorials for the NMR challenge.
  2. Small molecule NMR analysis of progesterone.[1]
  3. Small molecule NMR analysis of ubiquitin.[1]

Capstone Presentation- Drugs and Targets

Potentially Useful Information

  • I have had native speakers in Chinese (several) and Italian attest to the accuracy of DeepL Translate to translate English into their native languages.
  • I have had a native speaker attest to the accuracy of Yandex to translate English into Arabic.
  • For speaking text in various languages, AWS Polly seems to be the best.
  • Chemical Class versus a Drug Class

Old

References and Notes

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