Factors limiting the performance of prediction‐based fold recognition methods

In the past few years, a new generation of fold recognition methods has been developed, in which the classical sequence information is combined with information obtained from secondary structure and, sometimes, accessibility predictions. The results are promising, indicating that this approach may compete with potential‐based methods (Rost B et al., 1997, J Mol Biol 270:471–480). Here we present a systematic study of the different factors contributing to the performance of these methods, in particular when applied to the problem of fold recognition of remote homologues.

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