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ProtScale - Help about parameter settings

ProtScale allows you to compute and represent 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 the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but many other scales exist which are based on different chemical and physical properties of the amino acids. This program provides 50 predefined scales entered from the literature.

You can set several parameters that control the computation of a scale profile, such as the window size, the weight variation model, the window edge relative weight value, and scale normalization.