SABIC

SABIC performs protein structure alignment using internal coordinates (bond lengths, bond angles, and torsion angles) to evaluate structural similarity among proteins.

Key Features:

• Internal Coordinate-Based Alignment: Aligns protein structures using internal coordinates—bond lengths, bond angles, and torsion angles—rather than Cartesian coordinates.
• Multi-Alignment Output: Generates multi-structure alignments for comparative analysis across multiple proteins.
• Performance Superiority: Benchmark evaluations on reference datasets report higher accuracy and reliability than DALI, CE, and SSM.
• mQ-Score for Alignment Quality: Computes an mQ-score as a quantitative metric to assess alignment quality and structural similarity.
• Statistical Significance Assessment: Fits an extreme value distribution to mQ-scores to compute P-values that evaluate the statistical significance of alignments.

Scientific Applications:

• Fold Mechanism Analysis: Supports analysis of protein folding mechanisms by comparing intrinsic geometric parameters across structures.
• Evolutionary History Investigation: Facilitates investigation of evolutionary relationships by detecting conserved structural similarities.
• Functional Annotation: Assists functional annotation by identifying conserved structural motifs via multi-structure alignments and quality metrics.

Methodology:

Performs internal-coordinate alignment based on bond lengths, bond angles, and torsion angles; computes mQ-scores and fits their extreme value distribution to assign P-values; implemented in C++.