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Structural Bioinformatics, 2nd Edition by Philip E. Bourne, Jenny Gu

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12

THE NUCLEIC ACID DATABASE

Bohdan Schneider, Joanna de la Cruz, Zukang Feng, Li Chen, Shuchismita Dutta, Irina Persikova, John D. Westbrook, Huanwang Yang, Jasmine Young, Christine Zardecki, and Helen M. Berman

INTRODUCTION

The Nucleic Acid Database (NDB) (Berman et al., 1992) was established in 1991 as a resource for specialists in the field of nucleic acid structure. Over the years, the NDB has developed generalized software for processing, archiving, querying, and distributing structural data for nucleic acid containing structures. The core resource of the NDB has been its relational database of nucleic acid containing crystal structures; now the database has incorporated structures derived by both X-ray crystallography and methods of NMR spectroscopy. Recognizing the importance of standard data representation in building a database, the NDB became an active participant in the mmCIF project and provided the test bed for this format. From a foundation of well-curated data, the NDB created a searchable relational database of primary and derivative data with very rich query and reporting capabilities. This robust database was unique in that it allowed researchers to make comparative analyses of nucleic acid containing structures selected from the NDB by means of the many attributes stored in the database.

In 1992, the NDB assumed responsibility for processing all nucleic acid crystal structures that were deposited into the PDB, and in 1996, it became a direct deposit site. To ...

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