Is it a paradox or misinterpretation?

The paradox recently raised by Wang and Yuan (Proteins 2000;38:165-175) in protein structural class prediction is actually a misinterpretation of the data reported in the literature. The Bayes decision rule, which was deemed by Wang and Yuan to be the most powerful method for predicting protein structural classes based on the amino acid composition, and applied by these investigators to derive the upper limit of prediction rate for structural classes, is actually completely the same as the component-coupled algorithm proposed by previous investigators (Chou et al., Proteins 1998;31:97-103). Owing to lack of a complete or near-complete training data set, the upper limit rate thus derived by these investigators might be both invalid and misleading. Clarification of these points will further stimulate investigation of this interesting area. Copyright 2001 Wiley-Liss, Inc.