ASC-G4

ASC-G4 calculates advanced structural characteristics of G-quadruplexes (G4) to unambiguously determine intramolecular topology and provide detailed geometric and stereochemical parameters for structural analysis.

Key Features:

• Topology Determination: Identifies intramolecular G4 topology and resolves ambiguities in topology assignment.
• Oriented Strand Numbering: Employs oriented strand numbering to enhance precision in structural analysis.
• Guanine Glycosidic Configuration: Determines guanine glycosidic (syn/anti) configurations within tetrads and strands.
• Groove Width Calculation: Calculates groove widths using C3' or C5' atom coordinates and emphasizes minimum groove width as an indicator of spatial constraints, preferring these over phosphate (P) atoms.
• Loop Characterization: Reports loop types and lengths for intramolecular G4s.
• Snapbacks and Bulges Detection: Identifies presence of snapbacks and bulges within G4 structures.
• Guanine Distribution: Determines guanine distribution across tetrads and strands.
• Geometric Parameters: Computes rise angles, tilt and twist angles, and backbone dihedral angles.
• Distance Metrics: Provides atom–atom and atom–plane distances for structural assessment.

Scientific Applications:

• Structural Analysis: Provides detailed topology, loop characterization, snapback and bulge identification, and guanine distribution for G4 structural studies.
• Molecular Geometry: Supplies glycosidic configurations, rise, tilt and twist angles, groove widths (including minimum values), and backbone dihedral angles for geometric analysis.
• Quality Evaluation: Delivers atom–atom and atom–plane distance metrics useful for assessing the quality and stereochemical consistency of G4 structures.

Methodology:

Computations use oriented strand numbering to determine intramolecular topology and guanine glycosidic configurations; groove widths are calculated from C3' or C5' atom coordinates (preferred over phosphate (P) atoms), and the algorithm was validated on 207 G4 structures.