CSCI2951-G Computational Protein Folding
Fall 2012, Monday 1-1:50 and Wednesday 12-1:50, CIT 506.
Instructor: Paul Valiant
Announcements:
Posted Thursday, September 27: There are currently three things due. Assignment 2 ("implement physics") is due Monday, October 1; the chapter 2 reading is due Wednesday, October 3; assignment 3 ("arranging atoms") is due Wednesday, October 10.
The textbook is now on reserve at the Science Library, where you can borrow it for 24 hour periods.
Handouts:
Class 1 (September 6):
Notes from class 1
Course Description
Homework 0
Source code for homeworks
Class 2 (September 10):
Notes from class 2
Class 3 (September 12):
Homework 1
Guide to the proteins code
Reading from the textbook due Wednesday, September 19: page 1; pages 7-9 (section 1.1.3 but stop before 1.1.3.1.3); and pages 36-59 (section 1.2 to the end of the chapter). Feel free to skim section 1.1 if you feel you want more detail about why proteins are important for life, but it gets bogged down in a lot of chemistry that really doesn't have much to do with protein folding.
Class 4 (September 17):
Notes from classes 3 and 4
Class 5 (September 19):
Notes from class 5
Homework 3 (!)
Class 6 (September 24):
Notes from class 6
Homework 2
Class 7 (September 26):
Reading and questions due Wednesday, October 3:
Section 2.1 but stop before 2.1.2 (1.5 pages); Pages 79-81; Section 2.3 to before 2.4.2.1.1 (bottom of p. 103 to mid p. 132); Box 2.5 p. 149; Section 2.4.3.2 (2 pages); Section 2.5 but stop before 2.5.2 (1 page); Section 2.6 but stop before 2.6.2 (1 page).
Turn in answers to the following:
What is a hydrogen bond (in the language of our force field)? (one sentence)
An alpha helix contains hydrogen bonds between which atoms? (one or two sentences)
What does it mean for a protein to be "water-soluble"? (one or two sentences)
What is the role of entropy in this reading? (100-200 words)