A critical assessment of the secondary structure prediction of α-helices and their termini in proteins

ISSN: 02692139
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Abstract

Secondary structure prediction from amino acid sequence is a key component of protein structure prediction, with current accuracy at ∼75%. We analysed two state-of-the-art secondary structure prediction methods, PHD and JPRED, comparing predictions with secondary structure assigned by the algorithms DSSP and STRIDE. The specific focus of our study was α-helix N-termini, as empirical free energy scales are available for residue preferences at N-terminal positions. Although these prediction methods perform well in general at predicting the α-helical locations and length distributions in proteins, they perform less well at predicting the correct helical termini. For example, although most predicted α-helices overlap a real α-helix (with relatively few completely missed or extra predicted helices), only one-third of JPRED and PHD predictions correctly identify the N-terminus. Analysis of neighbouring N-terminal sequences to predicted helical N-termini shows that the correct N-terminus is often within one or two residues. More importantly, the true N-terminal motif is, on average, more favourable as judged by our experimentally measured free energies. This suggests a simple, but powerful, strategy to improve secondary structure prediction using empirically derived energies to adjust the predicted output to a more favourable N-terminal sequence.

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Wilson, C. L., Hubbard, S. J., & Doig, A. J. (2002). A critical assessment of the secondary structure prediction of α-helices and their termini in proteins. Protein Engineering, 15(7), 545–554.

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