Welcome to the NDB
Important Notice: The Nucleic Acid Knowledgebase (nakb.org), a new web-based data resource for experimentally-determined structures containing DNA and RNA nucleic acid polymers and their biological assemblies, is the planned successor to NDB (see Berman, Lawson & Schneider (2022), Developing Community Resources for Nucleic Acid Structures. Life 12, 540, DOI). NAKB preserves all of the functionality of NDB, including search, tabular reports, statistics, 2D and 3D visualization tools, education and standards pages, and a nucleic-acid community web and software resource list.
This website (ndbserver.rutgers.edu) will be retired in early July 2023. At that time, all NDB web traffic will forward to nakb.org. Links to individual entry NDB atlas pages will redirect to NAKB atlas pages. Questions/comments? please contact ndbadmin@ndbserver.rutgers.edu.
Search DNA
Search DNA and its complexes
Search RNA
Search for RNA structures in the NDB archive or in the Non-Redundant list
Advanced Search
Search for structures based on structural features, chemical features, binding modes, citation and experimental information
RNA 3D Motif Atlas, a representative collection of RNA 3D internal and hairpin loop motifs
Non-redundant Lists of RNA-containing 3D structures
RNA Base Triple Atlas, a collection of motifs consisting of two RNA basepairs
WebFR3D, a webserver for symbolic and geometric searching of RNA 3D structures
R3D Align, an application for detailed nucleotide to nucleotide alignments of RNA 3D structures