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

Haghighi, H. and Higham, J. and Henchman, R.H. (2016) Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure. Journal of Physical Chemistry B, 120 (33). pp. 8566-8570. ISSN 1520-6106

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.