CMSC 27610 Digital Biology Homework.

Exercises are to be handed in at the beginning of class two meetings after the assignment date, that is in general, one week later.

• Assignment date: task to be done.

• Thursday 5 Jan: Read chapters 1 and 2.
• Tuesday 10 Jan: Do exercises 2.3 and 2.4 and read chapter 3
• Thursday 12 Jan: Read chapter 4.
• Tuesday 17 Jan: Do exercises 3.5 and 4.5 and read chapter 5
• Thursday 19 Jan: Re-do first programming assignment and read chapter 6
• Tuesday 24 Jan: Do exercises 4.8 and 5.4 (due Tuesday 31 Jan) and read chapter 7
• Thursday 26 Jan: read chapter 8
• Tuesday 31 Jan: Do the following exercises (due Tuesday 14 Feb) and read chapters 10, 11 and 12
  • Consider the distribution of distances between CA carbons separated in sequence by k=2 in a given PDB file. Explain the bimodal character in PDB file 2P9R. Correlate the distance with phi and psi angles.
  • Correlate the distances between CA carbons separated in sequence by k with the secondary structure call in a given PDB file. That is, give the (three, separate) distributions of distances as a function of k for helices and sheets and loops (that is, for residues not in either structure).
  • (redo of Ex 5.4) Determine whether the choice of atom XG (resp. XD) in (5.6) matters for Asp (resp. Glu) by examining high-resolution structures. For each Asp (and Glu), compute the difference of dihedral angles for the two choices of terminal atoms, and plot the distribution of angle distances, in degrees.
  • Ex 8.3
  • Exercise 10.15
• Tuesday 14 Feb: read chapter 12
• Thursday 16 Feb: read chapter 13 and do Exercise 12.3 (due Thursday 23 Feb). More precisely, look for instances separately for Phe, Tyr and Trp. Limit the class of hydrogen bond donors to mainchain donors and NH groups on Asn and Gln, and give the distributions of the mainchain and sidechain donors separately. (This means six different distributions.) Use (6.1) to determine hydrogen placement for the former and (6.2-3) for the latter. Use the subset of the non-redundant PDB (nrpdb) on the class web page.