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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.

Author information

1
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.

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.

PMID:
19474339
PMCID:
PMC2703980
DOI:
10.1093/nar/gkp358
[Indexed for MEDLINE]
Free PMC Article

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