title: Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence.
abstract: Existing approaches to protein secondary structure prediction from the amino acid sequence usually rely on the statistics of local residue interactions within a sliding window and the secondary structural state of the central residue. The practically achieved accuracy limit of such single residue and single sequence prediction methods is 65% in three structural stages (alpha-helix, beta-strand and coil). Further improvement in the prediction quality is likely to require exploitation of various aspects of three-dimensional protein architecture. Here we make such an attempt and present an accurate algorithm for secondary structure prediction based on recognition of potentially hydrogen-bonded residues in a single amino acid sequence. The unique feature of our approach involves database-derived statistics on residue type occurrences in different classes of beta-bridges to delineate interacting beta-strands. The alpha-helical structures are also recognized on the basis of amino acid occurrences in hydrogen-bonded pairs (i,i + 4). The algorithm has a prediction accuracy of 68% in three structural stages, relies only on a single protein sequence as input and has the potential to be improved by 5-7% if homologous aligned sequences are also considered.
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: D
authors.initials: D
authors.lastname: Frishman
authors.forename: P
authors.initials: P
authors.lastname: Argos
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003195:Computer Communication Networks; D006860:Hydrogen Bonding; D007256:Information Systems; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D012984:Software