3DNALandscapes

3DNALandscapes provides a searchable database of DNA conformational parameters and molecular images computed with the 3DNA software for all DNA-containing structures in the Protein Data Bank (PDB).

Key Features:

• Extensive Structural Parameter Collection: Contains a broad spectrum of structural parameters and molecular images computed with 3DNA that characterize the sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, and groove structures.
• Integration with the Protein Data Bank (PDB): Incorporates data from all DNA-containing PDB entries, including free DNA and DNA bound to proteins, drugs, and other ligands.
• Cross-Structure Search and Comparative Analysis: Enables searches across multiple DNA structures to examine sequence-dependent conformational diversity, deformability, and conformational rearrangements.
• Benchmarking and Simulation Support: Provides datasets from well-resolved DNA structures that serve as benchmarks for analyzing and simulating DNA configurations and responses to molecular interactions or environmental conditions.

Scientific Applications:

• Characterization of Sequence-Dependent Conformational Features: Enables analysis of how specific nucleotide sequences influence spatial arrangements and structural parameters.
• Study of DNA-Protein Interactions: Supports investigation of protein recognition and binding by comparing DNA conformations in DNA–protein complexes.
• Investigation of Ligand Binding Effects: Facilitates analysis of conformational changes induced by drugs and other ligands bound to DNA.
• Analysis of Conformational Dynamics: Allows examination of DNA deformability and structural rearrangements under different interaction contexts.

Methodology:

Structural parameters and molecular images are computed with the 3DNA software package from DNA-containing entries in the PDB and provided to enable cross-structure searches and comparative analysis.