Secondary structure assignment is an important task in protein structure analysis and modeling. There are still large discrepancies among the dozens of available methods, especially in the distinction of helix types and identification of rare secondary structures. Classification is subject to ambiguity and inaccuracies due to the employment of empirical energy functions and/or imprecise parameter ranges. We have developed a new method for secondary structure classification, termed QUESSO, based on local helix parameters, quaternion analysis, and energy criteria derived from QM calculations. Secondary structures are associated with distinct energy minima in the potential energy surface (PES) of a virtually infinite polyalanine chain. The values of the local helix parameters can be then unequivocally associated with a secondary structure based on the energy gradient. QUESSO identifies α-, 310-, π- and γ-helices, PP-II helix, and β-strand and their handedness unambiguously. QUESSO compared favorably to DSSP, STRIDE, and others, showing good agreement in the core of helices and strands. However, QUESSO yielded better discrimination of helix types, secondary structure termini, and accounted for irregularities. QUESSO and the underlying mathematical definitions are robust enough to provide a consistent assignment similar to hydrogen- bond based methods. Geometry distortions are avoided thus producing more uniform helices and strands. QUESSO is a comprehensive and precise method that provides
a detailed characterization of protein structure.

QUESSO: Quaternion-based and first principles energy-driven protein secondary structure output

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