A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 14-Jul-2023 number of released structures: 12873
Search for released structures

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.
The NDB website (ndbserver.rutgers.edu) has been retired as of July 15, 2023 and for a time is available as an archived site here (ndb-archive.rcsb.rutgers.edu).. All NDB web traffic now forwards to nakb.org. Links to individual entry NDB atlas pages are redirected to NAKB atlas pages. Questions/comments? please contact help@nakb.org


Search Structures

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



Featured Tools

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