The illustration of the differences in assignment by our algorithm and dssp.

<p>In (a) dssp assigns the entire segment (51–65, excluding P50) in a protein (pdbid 3OY9) as an <i>α</i>-helix. Our algorithm divides it into two helices: 3₁₀-helix (51–52, red) and <i>α</i>-helix (53–63, green, purple, yellow). The <i>α</i>-helix stops at N63 since the C_<i>α</i> RMSD <i>δ</i> values for residue 64 and 65 are respectively 0.541, 0.431, none of them less than <i>d</i>_<i>max</i> = 0.3. In contrast, the dssp assigned helix extends to residue 65. However, as shown in the left figure, the C_<i>α</i> coordinates of both residue 64 and 65 deviate clearly from a helical curve. In (b) a segment of residues 153–172 in a protein (pdbid 1MHY) is assigned as a single <i>α</i>-helix by dssp while our algorithm divides it into four helices: 3₁₀-helix(154–156, yellow)–<i>α</i>-helix(157–163, green)–3₁₀-helix(164–166, purple)–<i>α</i>-helix(167–171, green). However, a careful examination of the hydrogen bond energies for these residues in fact suggests that they could also be assigned to a 3₁₀-helix even by the dssp standard (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129674#pone.0129674.s002" target="_blank">S2 Fig</a>).