Nucleic Acids Research Advance Access originally published online on May 27, 2009
Nucleic Acids Research 2009 37(Web Server issue):W240-W246; doi:10.1093/nar/gkp358
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W240-W246
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures
1Rutgers, the State University of New Jersey, Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ 08854 and 2Department of Biological Sciences, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10027, USA
*To whom correspondence should be addressed. Tel: +1 732 445 3993; Fax: +1 732 445-5958; Email: wilma.olson{at}rutgers.edu
Received March 2, 2009. Revised April 14, 2009. Accepted April 22, 2009.
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.
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