Quantitative comparison of the ability of hydropathy scales to recognize surface beta-strands in proteins

Methods based on the use of hydropathy scales have been used widely to ascertain the secondary structures of proteins. However, over 100 such scales have been reported in the literature, and which of these is the most successful in terms of the prediction rate of the correct structure is not clear. This article, therefore, reports a comprehensive analysis of the relative success of hydropathy scales to locate beta-strands on the surfaces of proteins. The technique we used is based on the technique proposed by Fraser and Parry, but it includes a modification that allows a higher rate of successful prediction and a lower rate of overprediction. We used as a basis for assessing the predictions a database of sequence-unique structures that we previously established. Proteins 2001;42:243-255.