Journal
NUCLEIC ACIDS RESEARCH
Volume 37, Issue -, Pages W240-W246Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkp358
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Funding
- U.S. Public Health Service [GM20861, RR022375, DK071502]
- Mary I. Bunting Fund of Rutgers
- State University of New Jersey
- NATIONAL CENTER FOR RESEARCH RESOURCES [S10RR022375] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES [R90DK071502] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM020861, R37GM020861] Funding Source: NIH RePORTER
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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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