Protein Engineering, Vol. 15, No. 7, 545-554,
July 2002
© 2002 Oxford University Press
A critical assessment of the secondary structure 
-helices and their termini in proteins
Department of Biomolecular Sciences, UMIST, P.O. Box 88, Manchester M60 1QD, UK
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 
-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 -helical locations and length distributions in proteins, they perform less well at predicting the correct helical termini. For example, although most predicted -helices overlap a real -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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