Computationele Biochemie

Vakinformatie

Nieuw vak vanaf 2025-2026.

Examenvragen

8/06/2026 (VM)

1. Kleine problem set (zelf code schrijven): Hamming Distance
2. Big problem set (Code gegeven en vragen erover beantwoorden): Manhattan Tourist Problem using Top-Down dynamics with memoization and path traceback
   1. Explain the role of 'self.memo' (explain what information is stored in 'self.memo', why the keys are tuples such as (i,j), and how this changes the efficiency of the recursive solution.

   Bijvragen:

   • what would happen if we remove 'self.memo'
   • What is 'self.memo'?
   • what kind of information stores 'self.memo' (possibilities: string, ...)

   1. Identify the base cases and the recursive cases in 'MTP(i,j)', and explain why they are necessary (distinguish clearly between the starting condition of the recursion, the condition that prevents the algorithm from leaving the grid and the part that reduces the problem to smaller subproblems)

   Bijvragen:

   • Why -1 and not 0 (for the part that prevents the algorithm from leaving the grid)

   1. Explain how the algorithm finds not only the optimal score but also the optimal path. (Describe the roles of 'up', 'left', ' diagonal', 'self.path', and 'get.path()'. The answer should make clear why the following stored predecessors reconstruct an optimal path.

   Bijvragen:

3. Groups project

   • GP3 (raw and minimised torsion angle comparison)

   1. • explain Ramachandran and Janin plot

   • what is put on which axis
   • what is the difference between them

   1. • give the atoms that define phi and psi
      • where in the plot is the beta-sheet and why
      • explain the given code (here, the code was the one from the dehidral angle)

   • what do v1, v2, v3, n1 and n2 represent
   • what makes up a "vlak"

   1. • given 3 Ramachandran plots (raw, minimised and overlay)

   • Do these plots represent 1 protein or a protein set?
   • When would we use these plots? What are they used for?