Homework 3: (Due Thursday, 09/20)

• Extract the protein coded 1mbc from the protein data bank.
• Read the C_a coordinates into MATLAB.
• Check and report deviation from an ideal distance between the C_a (create a graph of the deviation from the ideal distance as a function of the amino acid index).
• Create a cubic spline fit to the data.
• Use the cubic spline to estimate the curvature of the protein chain. The curvature is defined as the rate of change of the direction of a unit vector along the path. That is, let ê be a unit vector parallel to the path direction; the curvature is defined as |dê/dt|. Can you find correlation between the curvature and the secondary structure?
• Analyze the secondary structure of 1mbc using a contact matrix.