title: Limits on alpha-helix prediction with neural network models.
abstract: Using a backpropagation neural network model we have found a limit for secondary structure prediction from local sequence. By including only sequences from whole alpha-helix and non-alpha-helix structures in our training and test sets--sequences spanning boundaries between these two structures were excluded--it was possible to investigate directly the relationship between sequence and structure for alpha-helix. A group of non-alpha-helix sequences, that was disrupting overall prediction success, was indistinguishable to the network from alpha-helix sequences. These sequences were found to occur at regions adjacent to the termini of alpha-helices with statistical significance, suggesting that potentially longer alpha-helices are disrupted by global constraints. Some of these regions spanned more than 20 residues. On these whole structure sequences, 10 residues in length, a comparatively high prediction success of 78% with a correlation coefficient of 0.52 was achieved. In addition, the structure of the input space, the distribution of beta-sheet in this space, and the effect of segment length were also investigated.
authors.affiliation: Biocomputing Research Unit, Institute of Cell and Molecular Biology, Edinburgh, Scotland.
authors.forename: S
authors.initials: S
authors.lastname: Hayward
authors.forename: J F
authors.initials: JF
authors.lastname: Collins
mesh_terms: D000595:Amino Acid Sequence; D005544:Forecasting; D008432:Mathematical Computing; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D009842:Oligopeptides / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D009842:Oligopeptides; D011506:Proteins