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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp959
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

3DNALandscapes: a database for exploring the conformational features of DNA

Guohui Zheng1, Andrew V. Colasanti1, Xiang-Jun Lu1,2 and Wilma K. Olson1,*

1Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, 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 August 15, 2009. Revised October 10, 2009. Accepted October 13, 2009.

3DNALandscapes, located at: http://3DNAscapes.rutgers.edu, is a new database for exploring the conformational features of DNA. In contrast to most structural databases, which archive the Cartesian coordinates and/or derived parameters and images for individual structures, 3DNALandscapes enables searches of conformational information across multiple structures. The database contains a wide variety of structural parameters and molecular images, computed with the 3DNA software package and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, groove structure, etc. The data comprise all DNA-containing structures—both free and bound to proteins, drugs and other ligands—currently available in the Protein Data Bank. The web interface allows the user to link, report, plot and analyze this information from numerous perspectives and thereby gain insight into DNA conformation, deformability and interactions in different sequence and structural contexts. The data accumulated from known, well-resolved DNA structures can serve as useful benchmarks for the analysis and simulation of new structures. The collective data can also help to understand how DNA deforms in response to proteins and other molecules and undergoes conformational rearrangements.


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