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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W240-6. doi: 10.1093/nar/gkp358. Epub 2009 May 27.

Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.

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Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Wright-Rieman Laboratories, Rutgers, State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, USA.


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, including their complexes with proteins and other ligands. The server allows the user to determine a wide variety of 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, etc. It is also possible 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. The visualization component offers unique, publication-quality representations of nucleic-acid structures, such as 'block' images of bases and base pairs and stacking diagrams of interacting nucleotides. The w3DNA web server, located at, is free and open to all users with no login requirement.

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