Web 3DNA

The w3DNA (web 3DNA) server is a user-friendly web-based interface to the 3DNA suite of programs for the analysis, reconstruction, and visualization of three-dimensional (3D) nucleic-acid-containing structures. It offers a wide range of features that allow users to determine various conformational parameters in a given structure, such as the identities and rigid-body parameters of interacting nucleic-acid bases and base-pair steps, the nucleotides comprising helical fragments, among others.

One of the most interesting features of the w3DNA server is the ability to build 3D models of arbitrary nucleotide sequences and helical types, customized single-stranded and double-helical structures with user-defined base-pair parameters and sequences, and models of DNA 'decorated' at user-defined sites with proteins and other molecules. This makes it an invaluable tool for researchers studying the structure and function of nucleic acids, particularly in the context of their interactions with other biomolecules.

The visualization component of the w3DNA server is also noteworthy, as it offers unique and publication-quality representations of nucleic-acid structures. For example, it allows users to generate 'block' images of bases and base pairs and stacking diagrams of interacting nucleotides. These visualizations can be incredibly useful for understanding the structure and function of nucleic acids, as well as for communicating research findings to others in the field.