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

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• The Define Secondary Structure of Proteins (DSSP) algorithm is the standard for protein secondary structure assignment.
• DSSP relies on hydrogen bond definitions with energy cutoffs, potentially limiting its generality.

Purpose of the Study:

• To evaluate a parameter-free hydrogen bond definition for protein secondary structure assignment.
• To assess the accuracy and generality of the SABLE method compared to DSSP.

Main Methods:

• Examined various hydrogen bond definitions for secondary structure assignment across multiple proteins.
• Developed and applied the SABLE (strongest-acceptor bifurcated) method, accounting for unassigned donor hydrogens.

Main Results:

• The SABLE method demonstrated 95% agreement with DSSP assignments.
• Discrepancies primarily occurred in regions like helices, turns, and bends.
• The SABLE method avoids molecule-specific cutoff parameters.

Conclusions:

• Parameter-free hydrogen bond definitions can generalize secondary structure assignment methods.
• SABLE offers a promising alternative to DSSP, enhancing applicability across diverse hydrogen-bonded systems.