Figure 1.

From the 3 D structure to the 1 D structural sequence. A protein structure is decomposed into overlapping four-residue fragments (A). Each fragment is described by a vector of four descriptors d₁, d₂, d₃ and P₄ (B) allowing their comparison to the 27 structural letters of the HMM-SA alphabet presented in (C) where α-letters (red frame), β-letters (green frame), borders-letters associated with helix-borders (red dotted frame) and to strand-borders (green dotted frame) and loop-letters (black frame) are indicated. The encoding of a 3 D structure into the structural sequence (D) takes into account both the similarity of the protein fragments with the 27 structural letters and the preferred succession of the structural letters.