Assignments for week 2

Secondary structure prediction and membrane protein structure predictions.

Usefull Links For This Week

• The course 96 list of links. You can find both secondary structure and membrane protein servers here.
• Added links during the course. If you find an interesting link please add it here.

Practical Reports

1. SECONDARY STRUCTURE PREDICTIONS.
• Use four different secondary structure prediction servers. Predict the secondary structure for the following proteins (pdb codes) Cytochrome B562 (256B), Fatty-acid Binding protein (1ifb) Plastocyanin (2pcy) myoglobin (1mbo) aglin C (1cse) and dihydrofolate reductase (3dfr). The sequences and correct secondary structure prediction can be found in this directory Submit the secondary predicted structures here
  Which secondary structure algorithm works best for each of these testcases ?
  The sequences can be found here.
  Which secondary structure prediction algorithms did you try (please include http addresses) ?
  
2. MEMBRANE PROTEIN PREDICTIONS.
• The structure of Cytochrome C Oxidase has recently been published. The sequence can be found here The observed secondary structure is found here. Note that "H" symbolises a transmembrane helix and "h" a non-transmembrane helix. How good are the different prediction methods ?
  
  Which membrane structure prediction servers did you use ?
  
  

To understand before the reading seminars.

1. Describe the different type of algorithms used for secondary structure predictions.
   
2. What is the highest accuracy obtained for secondary structure predictions, for one sequence, and for multiple sequence alignments



3. Describe the different methods used for membrane protein structure predctions.


4. Why is membrane protein structure prediction harder, easier than predicting the structure of soluble proteins ?


5. What is the use of helical wheels ?