title: Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure.
abstract: DSSP is the most commonly used method to assign protein secondary structure. It is based on a hydrogen-bond definition with an energy cutoff. To assess whether hydrogen bonds defined in a parameter-free way may give more generality while preserving accuracy, we examine a series of hydrogen-bond definitions to assign secondary structure for a series of proteins. Assignment by the strongest-acceptor bifurcated definition with provision for unassigned donor hydrogens, termed the SABLE method, is found to match DSSP with 95% agreement. The small disagreement mainly occurs for helices, turns, and bends. While there is no absolute way to assign protein secondary structure, avoiding molecule-specific cutoff parameters should be advantageous in generalizing structure-assignment methods to any hydrogen-bonded system.
authors.affiliation: Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom.|School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom.
authors.forename: Hasti
authors.initials: H
authors.lastname: Haghighi
authors.affiliation: Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom.|School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Higham
authors.affiliation: Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom.|School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Henchman
mesh_terms: D006859:Hydrogen / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D055672:Static Electricity
chemical_list: D006859:Hydrogen