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The average hydropathy score (GRAVY) was calculated using the hydrophobicity values obtained from the Kyte-Doolittle scale [46].
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The hydrophobicity of each interface is defined as an average of the hydrophobicity values of each interface residue assigned using the hydrophobicity scale [35].
We also observed that these types can be classified using the hydrophobicity of the amine.
Using the approximate free energy function, Eq. (2), and a continuous approximation for the hydrophobicity values h(A i ), it is possible to determine analytically the sequence with minimal energy subject to the constraint of constant normalized energy gap.
If we use RSCU to compute the COA, the third major axis could not discriminate the genes according to the hydrophobicity values.
We then tested the significance of a linear model that the FDRs depend on the hydrophobicity values (Supplementary Table S4).
Each of the nine regions was also analyzed for the hydrophobicity value based on Kyte and Doolittle [17].
The hydrophobicity of a protein was defined as ∑ i = 1 n H i n, with Hi denoting the hydrophobicity value of the amino acid at position i of a protein of n amino acids.
Therefore, as it is concluded in [ 13], those methods which are based on the same physical properties that determine translocon-mediated membrane insertion, by using properly scaled hydrophobicity values, may access the same level of prediction accuracy as the best statistical methods.
Hydrophobic moments were calculated using an online tool available at http://rzlab.ucr.edu/scripts/wheel/wheel.cgi using standard interface hydrophobicity values for each residue (Wimley and White, 1996; Wimley et al., 1996).
A sliding window average of hydrophobicity was calculated with a window length of 18 residues using the Kyte Doolittle hydrophobicity scale (Kyte and Doolittle, 1982).
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