A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 26-Jan-2023 number of released structures: 12597
Search for released structures

Welcome to the NDB

The NDB contains information about experimentally-determined nucleic acids and complex assemblies.
Use the NDB to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and learn about nucleic acids.

New: Try out the Nucleic Acid Knowledgebase (NAKB) server (beta release)

NAKB is the planned successor to NDB, as described in this article: Berman, H.M.; Lawson, C.L.; Schneider, B. Developing Community Resources for Nucleic Acid Structures. Life 2022, 12, 540. https://doi.org/10.3390/life12040540


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