Introducing the Nucleic Acid Knowledgebase
The Nucleic Acid Knowledgebase (nakb.org) is a new web-based data resource for experimentally-determined structures containing DNA and RNA nucleic acid polymers and their biological assemblies.
NAKB currently indexes 16,000 nucleic acid-containing structures derived from all major structure determination methods (X-ray, NMR, and cryo-electron microscopy), including all held by the Protein Data Bank (PDB), and 48 structures held only by the Nucleic Acid Database (NDB). The resource is updated weekly on Thursdays at noon, US Eastern time.
As the planned successor to NDB (see Developing Community Resources for Nucleic Acid Structures (2022) Life12: 540), NAKB preserves all of the functionality of the legacy service, including search, tabular reports, statistics, 2D and 3D visualization tools, education and standards pages, and a nucleic-acid community web and software resource list.
For each structure, core descriptive information gathered from PDB or NDB is integrated with annotations curated by NDB/NAKB and nucleic-acid centered external resources including RNACentral, Rfam, DNATCO, 3DFootprint, DNAproDB, and BGSU RNA equivalence classes. NAKB also provides interactive tables of nucleotide, base-pair, and base-pair step parameters (DSSR), 2D folding diagrams (RNAView, R2DT), and a 3D viewer (Mol*).
The legacy NDB website (ndbserver.rutgers.edu) will be retired in early July 2023. At that time, all NDB web traffic will forward to nakb.org. All links to individual entry NDB atlas pages will automatically redirect to NAKB atlas pages.
NAKB development is funded by National Institutes of Health R01GM085328. NDB has been funded in the past by the National Science Foundation and the Department of Energy.