title: 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.
authors.affiliation: Department of Information Technology, University of Turku, FI-20014 Turku, Finland. sahaja@utu.fi
authors.forename: Satu
authors.initials: S
authors.lastname: Jääskeläinen
authors.forename: Pentti
authors.initials: P
authors.lastname: Riikonen
authors.forename: Tapio
authors.initials: T
authors.lastname: Salakoski
authors.forename: Mauno
authors.initials: M
authors.lastname: Vihinen
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013499:Surface Properties
chemical_list: D011506:Proteins