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The three most widely used methods for the prediction of protein secondary structure from the amino acid sequence are tested on 62 proteins of known structure using a program package and data collection not previously available. None of these methods predicts better than 56% of the residues correctly, for a three state model (helix, sheet and loop). The algorithms of Robson et al. J. Mol. Biol. (1978) 120, 97-120 and Lim J. Mol. Biol. (1974) 88, 873-894 are the best of those tested. New methods, now under development, can be tested against this benchmark.
Kabsch et al. (Sun,) studied this question.