Prediction of protein secondary structure from amino acid sequence

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Abstract
The conformational parametersP k for each amino acid species (j=1–20) of sequential peptides in proteins are presented as the product ofP i,k , wherei is the number of the sequential residues in thekth conformational state (k=α-helix,Β-sheet,Β-turn, or unordered structure). Since the average parameter for ann-residue segment is related to the average probability of finding the segment in the kth state, it becomes a geometric mean of (P k )av=π(P i,k ) 1/n with amino acid residuei increasing from 1 ton. We then used ln(Pk)av to convert a multiplicative process to a summation, i.e., ln(P k ) av =(1/n)⌆P i,k (i=1 ton) for ease of operation. However, this is unlike the popular Chou-Fasman algorithm, which has the flaw of using the arithmetic mean for relative probabilities. The Chou-Fasman algorithm happens to be close to our calculations in many cases mainly because the difference between theirP k and our InP k is nearly constant for about one-half of the 20 amino acids. When stronger conformation formers and breakers exist, the difference become larger and the prediction at the N- and C-terminalα-helix orΒ-sheet could differ. If the average conformational parameters of the overlapping segments of any two states are too close for a unique solution, our calculations could lead to a different prediction.