SCOT

SCOT classifies protein secondary structure elements—including turns, right-handed α-, 310- and π-helices; left-handed α- and 310-helices; polyproline II helices; β-sheets; and kinks—using hydrogen-bond, geometric, and dihedral-angle criteria and computes Helix Purity values to differentiate helix classes for structural analysis.

Key Features:

• Secondary-structure repertoire: Assigns turns, right- and left-handed α- and 310-helices, π-helices, polyproline II helices, β-sheets, and kinks.
• Assignment criteria: Combines hydrogen-bond detection, geometric criteria, and backbone dihedral-angle analysis for secondary-structure assignment.
• Helix Purity values: Computes Helix Purity values to distinguish between helix classes.
• Structure-quality independence: Produces assignments that are reported to be independent of protein structure quality and flexibility.
• Benchmarking: Compared against DSSP, STRIDE, ASSP, SEGNO, DISICL, and SHAFT with evaluations on geometric consistency, protein structure quality, flexibility dependency, and impact on SSE-based structural alignments, demonstrating superior performance.
• Output format: Exports results in PDB conform format.
• Visualization support: Provides PyMOL scripts for visualization of regular backbone geometries.

Scientific Applications:

• Structural analysis: Provides detailed and consistent secondary-structure assignments for protein structural analysis.
• Structural alignment: Improves secondary-structure-element-based structural alignments by supplying geometrically consistent SSE definitions.
• Prediction and annotation: Supports secondary-structure-based prediction and annotation workflows.
• Visualization of backbone geometry: Enables visualization of regular backbone geometries via supplied PyMOL scripts.

Methodology:

Assignments combine hydrogen-bond detection, geometric criteria, and backbone dihedral-angle analysis and compute Helix Purity values; outputs are produced in PDB conform format and PyMOL scripts are provided for visualization.