ONQUADRO

ONQUADRO aggregates and annotates structural and geometric data of nucleic acid G-quadruplexes, including tetrads, quadruplexes, and G4-helices from experimentally determined 3D structures to support structural and statistical analysis.

Key Features:

• Comprehensive Data Collection: ONQUADRO aggregates detailed information about 1,661 tetrads, 518 quadruplexes, and 30 G4-helices derived from 467 experimentally determined 3D nucleic acid structures (PDB) as of August 2021.
• Advanced Structural Analysis Tools: Includes programs to compute structural parameters and generate 2D and 3D graphical representations for qualitative and quantitative analysis.
• Detailed Descriptions: Provides sequence data, secondary structures represented in dot-bracket notation, classical diagrams, and arc diagrams, and tertiary structure visualizations as ball-and-stick, surface, van der Waals ball models, and layer diagrams.
• Motif-Specific Parameters: Reports planarity, twist, rise, chi angles (value and type), loop characteristics, strand directionality, and metal ion presence for motifs.
• Classification Systems: Employs the ONZ classification system and Webba da Silva geometric formalism to categorize loop topology and tetrad combinations.
• Statistical Analysis Tools: Provides scripts for statistical analysis of quadruplex structures.

Scientific Applications:

• Structural Characterization: Enables analysis of formation and geometric stability of tetrads, quadruplexes, and G4-helices.
• Functional Studies: Supports investigations into biological roles of quadruplexes, including interactions with proteins and small molecules.
• Therapeutic Development: Supports development of therapeutics targeting quadruplex structures implicated in diseases, including cancer.
• Comparative and Statistical Studies: Facilitates statistical and comparative analyses of quadruplex motifs across experimentally determined structures.

Methodology:

Data are obtained by downloading preliminary data from the PDB and then processed, annotated, and completed for integration into the database.