See here for a more recent evaluation ( Reference: Yang Y et al. Running a secondary structure prediction on a newly-determined sequence just because everyone else does so, is to be deplored, and the fact that the results of such predictions are generally ignored is insufficient justification for doing and publishing them." Arthur Lesk, 1988. This is true even of the best methods now known, and much more so of the less successful methods commonly available in sequence analysis packages.
Precautionary Quote: " We should be quite remiss not to emphasize that despite the popularity of secondary structural prediction schemes, and the almost ritual performance of these calculations, the information available from this is of limited reliability. Online Analysis Tools - Protein Secondary Structure PROTEIN SECONDARY STRUCTURE
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