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Alpha helix is a common type of secondary structure in the protein structure that consists of repeating helical turns. Patterns in the protein sequences that cause this repetitive pattern in the structure have long been sought. We used the discrete Fourier transform (DFT) to detect the periodicity signals correlated to the helical structure. We studied the distribution of multiple properties along the protein sequence, and found a property that showed strong periodicity correlated with the helical structure. Using a short-time Fourier transform (STFT) method, we investigated the amplitude of the periodical signals at each amino acid position. The results show that residues in the helix structure tend to display higher amplitudes than residues outside of the helices. This tendency is dramatically strengthen when sequence profiles obtained from multiple alignment were used to detect the periodicity. A simple method that predicted helices based on the amplitude yielded overall true positive rate (TPR) of 63%, 49% sensitivity, 72% specificity, and 0.22 Matthews Correlation Coefficient (MCC). The performance seemed to depend on the length of helices that the proteins had.

Detecting Periodicity Associated with the Alpha-Helix Structure Using Fourier Transform