The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids.

By Helen M. Berman, Wilma K. Olson, D. Beveridge, John D. Westbrook, A. Gelbin, Tamas Demeny, S. Hsieh, A. R. Srinivasan, B. Schneider. 1992

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Citations in the corpus

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning (2022, unknown): “NDB (100) Experimentally-determined nucleic acids and complex”
Automated 3D structure composition for large RNAs (2012, methodology): “To generate the structure, initial values of A-RNA torsion angles extracted from NDB (30) and distance restraints for the closure of sugar rings are applied.”
Joint X-ray and neutron refinement with phenix.refine. (2010, methodology): “Refinement of structures against neutron data alone To assess the impact of the tools specifically implemented for neutron refinement in phenix.refine, we reanalyzed 16 structures previously refined using neutron data (15 structures from the PDB and one from the NDB; Berman et al., 1992).”
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). (2008, background): “Even after the revolution in information content provided by the ribosome structures ( Ban et al. 2000; Wimberley et al. 2000; Schleunzen et al. 2000), most RNA backbone analyses have depended on some form of simplification: on plots for pairs of dihedrals (Kim et al. 1973; Murthy et al. 1999), on ”
MultiSeq: unifying sequence and structure data for evolutionary analysis (2006, unknown): “Structural data, even in the era of structural genomics, are produced at a slower pace but analyzed to a high degree before being deposited into the public databases, such as PDB [1], SCOP [2,3]/Astral [4], CATH [5] and NDB [6].”
An RNA-centric historical narrative around the Protein Data Bank (2021, methodology): “While the PDB remains, understandably, protein-centric, other databases and tools are available for nucleic acids (8, 12, 13)—see also https://www.”
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures (2019, methodology): “Over the years, 3DNA has been widely used, and adopted in many bioinformatics resources, including the NDB. 3DNA, along with Curves+ (6), is one of the most popular software products for the analysis of DNA/RNA double-helical structures.”
Tools for the automatic identification and classification of RNA base pairs (2003, methodology): “We selected 41 unique, well-refined X-ray crystal structures with resolutions of at least 3.0 Å from the current NDB database.”
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. (2003, background): “This simpli®ed, yet informative, image has been generated for each entry in the recently updated NDB atlas of structures (X.-J. Lu, W.K. Olson and H.M. Berman, unpublished data).”
MolProbity: all-atom structure validation for macromolecular crystallography (2009, unknown): “A typical MolProbity session starts with the user uploading a coordinate file of their own or fetching one from the PDB or NDB databases (Berman et al., 1992, 2000) in new or old PDB format or in mmCIF format.”