  Instead of conformation states of single residues, refined conformation
states of quintuplets are proposed to reflect conformation correlation. Simple
hidden Markov models combining with sliding window scores are used for
predicting secondary structure of a protein from its amino acid sequence. Since
the length of protein conformation segments varies in a narrow range, we ignore
the duration effect of the length distribution. The window scores for residues
are a window version of the Chou-Fasman propensities estimated under an
approximation of conditional independency. Different window widths are
examined, and the optimal width is found to be 17. A high accuracy about 70% is
achieved.
