Web 3DNA

Web 3DNA analyzes, reconstructs, and visualizes three-dimensional (3D) nucleic acid structures to quantify conformational parameters and build atomic models of DNA and their complexes with proteins and other ligands.

Key Features:

• Analysis Capabilities: Determines a wide range of conformational parameters including interacting nucleic-acid bases, base-pair steps, and the specific nucleotides composing helical fragments.
• Reconstruction Tools: Builds 3D models of arbitrary nucleotide sequences and various helical types, supporting customized single-stranded and double-helical structures with user-defined base-pair parameters and sequences.
• Model Customization: Constructs DNA models decorated at specific sites with proteins or other molecules to represent nucleic acid–protein and nucleic acid–ligand complexes.
• Visualization Features: Generates "block" images depicting bases and base pairs and produces stacking diagrams that illustrate nucleotide interactions.

Scientific Applications:

• Structural analysis: Quantifies and interprets conformational parameters of nucleic acid structures for structural biology and bioinformatics studies.
• Modeling nucleic acid complexes: Builds atomic models of DNA and nucleic acid–protein/ligand complexes for investigation of interaction interfaces.
• Functional and physical interpretation: Visualizes and models nucleic acid configurations to aid study of physical properties and functional mechanisms of DNA and its complexes.

Methodology:

Computes conformational parameters, identifies interacting nucleic-acid bases and base-pair steps, determines nucleotides composing helical fragments, constructs 3D models from arbitrary nucleotide sequences with user-defined base-pair parameters, assembles DNA models decorated with proteins or other molecules, and generates block images and stacking diagrams.