Modelling

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You were shown a simple model for secondary structure prediction, using a window size of 5 aminoacids to predict whether an aminoacid is part of an $\alpha$ -helix or not.

a) How many equations can be derived with this model given a sequence with a length of n aminoacids?

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b) Apply this simple model for secondary structure prediction to the following subsequence of Carboxypeptidase A:

primary structure	.....	S	V	D	D	E	A	Q	V	.....
secondary structure	.....	x	x	x	x	h	h	h	h	.....

Give the equations, which can be derived. Use the one-letter abbreviations of the Aminoacids and k (for constant bias) as variables.
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