# Biology
1. What is the central dogma of molecular biology
2. Which of N-C_{alpha}, N-C and C_{alpha}-C have the angles phi and psi?
3. Name 3 different forces for bonding in proteins
4. Name three different secondary structures
5. Alanine is replaced by valine and reduces activity. Then Isoleucine is replaced by glycene and activity is icreased again. Explain why.
# Monte Carlo
1. What is the outcome of a MC Algorithm that only picks better states
2. What are the two factors of the Metropolis Criterion?
3. An MC with Metrp. Crit. and high temperature finds the global optimum after a few steps. Will the algorithm stay there until the termination of the algorithm or will it move?
4. What is the idea behind simulated annealing?
5. How can one influence the exploratory vs. exploitory behaviour of different MC algorithms like MCMC and Simulated Annealing?
# Kinematics
1. A simple robot with two revolute joints and a prismatic joint is given. Compute the forward kinematics for (x,y,phi)
2. For a given configuration, write down the interpretation of a cell in the Jacobian
3. For a given configuration, write down the rank of J
4. Draw a configuration, where the rank of J = 2.
# Structure Prediction
Compare Comparative Modeling and Ab Initio Structure Prediction:
1. If you run both, what method would you choose depending on the results and what are the influencing factors?
2. What are general metrics to help deciding between choosing a method?
3. What are the four steps of comparative modeling
# Dynamic Programming
1. What is the biological motivation behind sequence alignment
2. What is the difference between local and global alignment
* Give Example
3. What is a substitution matrix?
4. How is a substitution matrix used in sequence alignment?
5. State the recursive formula of the smith-waterman algorithm
6. Fill in the table for two example strings and give the alignment result