ProtScale

ProtScale allows to compute and represent (in the form of a two-dimensional plot) the profile produced by any amino acid scale on a selected protein. An amino acid scale is defined by a numerical value assigned to each type of amino acid. The most frequently used scales are hydrophobicity scales, most of which were derived from experimental studies on partitioning of peptides in apolar and polar solvents, with the goal of predicting membrane-spanning segments that are highly hydrophobic, and secondary structure conformational parameter scales. In addition, many other scales exist which are based on different chemical and physical properties of the amino acids. ProtScale can be used with 50 predefined scales entered from the literature. The scale values for the 20 amino acids, as well as a literature reference, are provided on ExPASy for each of these scales. To generate data for a plot, the protein sequence is scanned with a sliding window of a given size. At each position, the mean scale value of the amino acids within the window is calculated, and that value is plotted for the midpoint of the window.