After this practical you will be able to:
Give three examples of the application simulated annealing: two in bioinformatics and one example in another area (not related to bioinformatics). For each example, briefly describe (i) how solutions are generated and (ii) how solutions are scored.
On page 972 of the article by Morris et al. (2002) the authors state: "The presence of cis-peptides adds an extra complication that we have chosen to ignore". Discuss this "complication", and why the authors chose to ignore it.
On page 219 of the article by Simons et al. (1997) the authors state: "the similarity in topology is clear ... in the contact map (Figure 9B)". Explain what the authors mean by this.
Suppose you want to reproduce the work of Chellapa and Rose (2012).
It is stated that "Eleven regions were abstracted from the plot and classified as labeled 20° × 20° basins". Describe how you might implement the step of abstracting basins from a plot.
Suppose you want to implement the step of "mapping each residue onto its corresponding basin". Describe how you might implement this step. Discuss practical issues that might need to be considered when implementing this step (e.g. consider whether the description in the paper is sufficiently clear to make implementation straightforward, or whether any additional assumptions or decisions are required).
Protein Data Bank entry 1QYS contains an crystal structure of the computationally designed protein Top7 (Kuhlman et al., 2003). Suggest 2 amino acid residue mutations that, for different reasons, might reduce the stability of Top7, or even prevent it from adopting a stable fold. Suggest another mutation that would be unlikely to affect the protein's stable fold. Give reasons to justify your choices.
You should submit your solutions as PDF or plain text via the Fire system before 23:59 on Monday 11 January 2016.
Everyone should do question 1. Those aiming for a higher grade should also attempt the other questions.