DNAproDB

DNAproDB provides structural analysis and standardized annotations of DNA–protein complexes by processing Protein Data Bank (PDB) entries to enable detailed mapping of nucleotide–residue interactions and chemically modified nucleotides.

Key Features:

• Extensive Database Coverage: Contains 95% of DNA–protein complexes from the Protein Data Bank (PDB).
• Support for Diverse DNA Structures: Supports B-form DNA, single-stranded DNA, and G-quadruplexes.
• Enhanced Data Processing Capabilities: Accommodates multiple DNA–protein complexes per entry and implements model indexing for ensemble data analysis.
• Visualization and Annotation: Generates nucleotide and residue interaction maps and assigns structural moieties for chemically modified residues and nucleotides with sequence-based annotations.

Scientific Applications:

• Structural Analysis: Enables atomic-level examination of DNA–protein interfaces and interaction patterns.
• Data Integration and Annotation: Integrates PDB structural data with sequence-based annotations and chemical modification assignments for comparative analyses.
• Visualization of Interactions: Produces interaction maps that support interpretation of complex DNA conformations and interface geometry.

Methodology:

Processes structural data from the PDB, integrates sequence-based annotations and chemical modification assignments, supports multiple DNA conformations and model indexing for ensemble analysis, and generates nucleotide/residue interaction maps.