title: Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.
abstract: 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 http://w3dna.rutgers.edu, is free and open to all users with no login requirement.
authors.affiliation: 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.
authors.forename: Guohui
authors.initials: G
authors.lastname: Zheng
authors.forename: Xiang-Jun
authors.initials: XJ
authors.lastname: Lu
authors.forename: Wilma K
authors.initials: WK
authors.lastname: Olson
mesh_terms: D003196:Computer Graphics; D004247:DNA / Q000737:chemistry*; D007091:Image Processing, Computer-Assisted; D020407:Internet; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D012313:RNA; D004247:DNA