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Welcome to 3DNALandscapes, a database for exploring the conformational features of DNA.
The database consolidates information about DNA deformations across ensembles of structures in combination with other currently available data resources. It is designed to provide a comprehensive survey and statistical analysis of DNA backbone, sugar-base side group, base-pair, base-pair-step, and complementary-strand arrangements, in the presence or absence of proteins, drugs, metals, water, and other molecules.
To get started with querying data, please use the Search component.
News and Updates:
08/15/2009The first release of the database contains derived information for all DNA-containing structures -- both free and bound to proteins, drugs, and other ligands -- deposited in the Protein Data Bank as of August 2009. The composite data come from 6602 structural models, taken from the complete sets of atomic coordinates reported in 2072 X-ray crystallographic and 586 NMR investigations. Among those structures, 1425 occur in complexes with proteins, 973 associate with drugs and other small molecules, and 2004 contain only bound water or metal ions. The X-ray-based entries reflect the coordinates of the biological units rather than the asymmetric structural units. Individual models within the ensembles of NMR-derived structures contain unique internal identifiers that are assigned as the database is loaded.
Improvements to the web interface allow users to specify their own choice of structures by inputting the PDB (Protein Data Bank) or NDB (Nucleic Acid Database) identifiers.
Improved grid-view tables with links to export data allow users conduct independent statistical analysis of the data downloaded from this site.
The construction of a database using the PHP Codeigniter package gives the user access to grid-view tables with sorting and paging capabilities.