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

DSSP is the most commonly used method to assign protein secondary structure. It is based on a hydrogen-bond definition with an energy cut-off. 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 is due to slightly more helices and beta bridges. While there is no absolute way to assign protein secondary structure, avoiding molecule-specific cut-off parameters should be advantageous in generalizing structure-assignment methods to any hydrogen-bonded system.