A refined accuracy index to evaluate algorithms of protein secondary structure prediction

Nowadays even a 1% increase of the accuracy for the secondary structure prediction is considered remarkable progress. In this case, we have to consider the reasonableness of the accuracy index Q(3), which is used widely. A refined accuracy index, called Q(8), is proposed to evaluate algorithms of secondary structure prediction. It is shown that Q(8) is superior to the widely used index Q(3) in that the former carries more information of the predictive accuracy matrix than does the latter. Therefore, algorithms are evaluated more objectively by Q(8) than Q(3). Based on 396 nonhomologous proteins, five currently available algorithms of secondary structure prediction were evaluated and compared using the new index Q(8). Of the five algorithms, PHD turned out to be the unique algorithm, with Q(8) accuracy better than 70%. It is suggested that Q(3) should be replaced by Q(8) in evaluating secondary structure prediction in future studies. Proteins 2001;43:520-522. (C) 2001 Wiley-Liss, Inc.