w3DNA

w3DNA provides analysis, visualization, and modeling of three-dimensional nucleic acid structures for structural bioinformatics studies.

Key Features:

• Integration of the 3DNA suite: Incorporates the latest 3DNA suite functionality for nucleic acid structural analysis and modeling.
• Automatic handling of modified nucleotides: Supports automatic recognition and incorporation of chemically modified nucleotides into structural analyses.
• Qualitative characterization tools: Provides 'simple' base-pair and step parameters for qualitative characterization of non-Watson-Crick double-helical structures.
• Advanced structural parameters: Implements parameters that integrate the rigid base plane and backbone phosphate group as determined by X-ray crystallography.
• In silico base mutations: Performs in silico base mutations while preserving nucleic acid backbone geometry during modeling.
• Model construction for diverse architectures: Constructs models of single-stranded RNA, double-helical DNA, Pauling triplexes, G-quadruplexes, and DNA structures decorated with proteins.
• Comprehensive 3D analysis and visualization: Combines analytical and modeling capabilities to produce three-dimensional representations and structural parameters of nucleic acids.

Scientific Applications:

• Genomics: Supports structural analyses that inform genomic studies by characterizing nucleic acid conformations.
• Epigenetics: Enables examination of chemically modified nucleotides relevant to epigenetic regulation.
• Structure-based drug design: Facilitates characterization of target nucleic acid conformations for rational drug design.
• Nucleic acid–protein interaction studies: Analyzes DNA structures decorated with proteins to investigate nucleic acid–protein interfaces.
• Canonical and non-canonical structure characterization: Characterizes canonical and non-canonical DNA/RNA forms including G-quadruplexes and Pauling triplexes.
• Disease mechanism investigation: Aids exploration of molecular mechanisms underlying biological processes and disease through structural analysis.

Methodology:

Uses command-line programs from the 3DNA suite to compute base-pair and step parameters, perform in silico mutations, and construct three-dimensional nucleic acid models.