== Aufgabe 1 == - What is Levinthals Paradox and how can one resolve it? - Name two properties Anfinsen postulated about Protein structures after his experiments on - What forces stablize a protein? - What requires more energy, a unraveling the alpha helix or destroying the beta sheet backbone, give a reason. == Aufgabe 2 == - What is co-evolutionary contact prediction? - Give three advantages of using distograms instead of contacts in protein structure prediction. - Give a (1) computational and (2) biological reason for using fragment libraries in protein structure prediction. - What is Metropolis Monte Carlo and simulated annealing and what is the reasoning behind using simulated annealing? == Augabe 3 == - Given a space where RRT was run 5 steps (you can see the already constructed tree) a) draw the voronoi diagram b) mark the point that is most likely to be extended - Describe two variants of RRT and reason, which one would perform better on the following problem: Close a loop with 50 joints - Why does the RRT make bigger extend steps when it starts, but smaller ones when it is almost done? == Aufgabe 4 == Given a robot arm with 3 roational joints - derive the forward kinematics of the end effector [x,y,theta]. - what is the meaning of J[2,2] where J is the Jacobian - calculate the entry of J[2,2] == Aufgabe 5 == The knapsack problem solved in a previous exrecise was 'hidden' in an exercise formulated such that vericula=bagpack, item=molecule, the volume=molecule size, value=toxicity, and vericula has a maximum volume, where is wants to maximize the toxicity - Formulate a recursive problem forumlation - what data structures to you need, write pseudo code to solve the problem - how could this problem be changed so that the DP does not work any more