Hybrid Protein Model (HPM): a method to compact protein 3D-structure information and physicochemical properties

The transformation of protein ID-sequence to protein 3D-structure is one of the main difficulties of the structural biology. A structural alphabet had been previously defined from dihedral angles describing the protein backbone as structural information by using an unsupervised classifier: The 16 Protein Blocks (PBs), basis element of the structural alphabet, allows a correct 30 structure approximation [6]. Local prediction herd been estimated by a Bayesian approach and shown that sequence information induces strongly The local fold, but stays coarse (prediction rare of 40.7% with one PB, 75.8% with the four most probable PBs). The Hybrid Protein Model presented in this study learns both sequence and structure of the proteins. The analysis made along the hybrid protein has permitted to appreciate more precisely the spatial location of same types of amino acid residues in the secondary structures and their flanking regions. This study leads to a fuzzy, model of dependence between sequence and structure.