Accuracy of protein hydropathy predictions

Abstract

Hydropathy is a dominant force in protein folding. Sequence-based hydropathy predictions are widely used, without knowledge about their accuracy and reliability. We investigated the prediction accuracy of 56 hydropathy scales by correlating predicted values with the accessible surface area in known protein structures. Results for different amino acids vary greatly within each scale. We also investigated prediction accuracies of amino acids separately in secondary structural elements and in protein fold families. Despite very low overall correlation, hydropathy predictions can still be used if the shape of the plot is important instead of the prediction values.