Calculation of the entropy profile
The latent entropy profile is calculated as follows. First, the number of degrees of freedom for the angles φ, ψ and χ is determined for each residue (see Number of degrees of freedom
), then the propensities for the residues inside the window are averaged and assigned to the central residue of the window. Therefore, the influence of residues along the sequence flanking each window is included in our calculation. The value of the average entropy parameter (the average number of degrees of freedom on the angles φ, ψ and χ) for every position of the polypeptide chain provides the latent entropy profile whose minima are predicted to correlate to domain boundaries (only the deepest minimum should be considered for two-domain proteins). We used a sliding window of 41 residues. This value was selected for two reasons. First, a domain should contain a hydrophobic core and should be larger than 40 residues. Second, this window size has been found to be the best compromise between a good resolution of the plot and a tolerable level of noise.