The Digital Nature of Biology

CMSC37701, Winter quarter 2008.

Homework

Here is an example of a rappa file

The PDB Select files are in /stage/cspp56410/pdb_select on the departmental machines. The corresponding rappa files are in /stage/cspp56410/pdb_select/rappa

Here is a zip file (17 MB, compressed) containing all of the rappa files for the PDBSelect proteins

• Homework due 11 Mar: Exercises 15.1, 15.2 and 15.6 from the notes.
• Homework due 26 Feb: Exercise 5.6 and exercise 12.1 from the notes.
• Homework due 14 Feb:
  • Helical secondary structure is formed by amide-carbonyl hydrogen bonding between peptides i and j where 2<|i-j|< 6. Determine how frequent it is to have i-j=k for the different possible values of k=-5,-4,-3,3,4,5. Are there instances where amide-carbonyl hydrogen bonding between peptides i and j where |i-j|=2 or |i-j|=6?
  • Also do Exercise 9.8 for 14 Feb.
• Homework due 22 Jan: Exercise 2.1 and Exercises 3.1 and 3.3

Some suggested projects:

• Exercise 5.4
• Exercise 5.7
• Exercise 7.5
• Exercise 12.3
• Exercise 13.1

Some Journals for the course.