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Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure

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<mark>Journal publication date</mark>25/08/2016
<mark>Journal</mark>Journal of Physical Chemistry B
Issue number33
Volume120
Number of pages5
Pages (from-to)8566-8570
Publication StatusPublished
Early online date12/04/16
<mark>Original language</mark>English

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.