Problem Sets and Exam Materials
Semester Review Paper assignment. Second draft due on Monday, 12/10.
Final Exam materials
- Review Guide for Final.
- Practice Exam from 2016. Note that this was a closed book/notes exam
- Solutions for the practice exam.
Problem Set #1x and Solutions.
- Some helpful stuff.
- And then also the azurin.pse PyMOL session file SerRS.pse PyMOL file.
Problem Set #10 is solely related to the paper by Coelho et al. (2013) on P450-catalyzed cyclopropanation. The supplemental is useful.
Problem Set #9 and Solutions.
- Some helpful links.
- We are reading the paper by Vocadlo et al. (2001) for class discussion on Tuesday next week. In addition, I've made a PyMOL file for the structure they solve: lysozyme.pse PyMOL session file
- You'll also need esterase.pse for problem #1...
- and Znsite.pse for problem #4...
Problem Set #8 and Solutions.
- Some helpful links.
- We are reading the paper by Fried et al. (2014) for class discussion on Tuesday next week. In addition, one question will relate to a comment published in response to the paper.
- And then also the KSI.pse PyMOL session file
Problem Set #7 and Solutions. You'll need the hemaglutanin.pse PyMOL session file.
Problem Set #6 and Solutions.
- Some helpful links.
- We are reading the paper by Wesener et al. (2015) for class discussion on
Thursday 10/25. It will help to look at the Supplemental materials. - And then also theROS.pse PyMOL session file for question 1 and lectin.pse for assistance with the paper.
Exam #1 materials and Solutions
- Review Guide for Exam 1.
- Practice Exam from 2016.
- Solutions for the practice exam.
Problem Set #5 and Solutions .
- Some helpful links.
- We are reading the paper by Rothemund (2006) for class discussion on Tuesday next week. It will help to look at the Supplemental materials especially Figure S1 and Note S9.
- And then also theZFbp.pse PyMOL session file for question 4 and 1HR2.pse for question 6 (there is no question 5 of course).
- Peng et al. (2015)Paper on KP1212 tautomers.
Problem Set #4 Questions and Solutions.
- Some helpful links.
- We are reading the paper by Cordes et al. (1999) for class discussion on Tuesday next week. A follow up paper in 2003 is here. It will help to look at the switch.pse PyMOL file. And for fun, you can also look at switch13.pse
- And then also theLLL.pse PyMOL session file for question 3.
- And then finally thetripeptide.pse PyMOL session file for question 4.
- Kleywegt and Jones (1995) Where freedom is given, liberties are taken!
Problem Set #3 and Solutions.
- Some helpful links.
- We are reading the paper by Luedtke et al. (2007) for class discussion on Tuesday next week. It will help to look at the gcn4.pse PyMOL file.
- And then also thecollagen.pse PyMOL session file for question 4
- Holmgren et al. (1999)Paper on substituted proline in collagen from Raines lab.
- Zhang et al. (2015) Paper on effect of azaglycine on collagen stability
Problem Set #2 and Solutions.
- Some links.
- Paper on helix crosslinking: Haney (2016) Org. Biomol. Chem., 14, 5768 with supplemental material
- PyMOL modeling exercise and download site for PyMOL
Problem Set #1 and Solutions.
- Some links.
- Quick Guide on how to read a scientific paper
- Chen et al. (2004)The Emergence of Competition Between Model Protocells, with supplemental materials
