2023-09-27 : 16739 3D structures containing nucleic acids | RNAEQ v3.302all
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NDB Co-founders

  • Helen M Berman, Rutgers University
  • Wilma K Olson, Rutgers University
  • David Beveridge, Wesleyan University

About NAKB and NDB

The Nucleic Acid Database (NDB) Project was founded in 1992, with the goal of archiving and distributing structural information about nucleic acids. The Nucleic Acid Knowledge Base (NAKB) is being developed as the planned successor to NDB. NDB/NAKB are funded by the National Institutes of Health R01 GM085328. NDB has been funded by National Science Foundation and the Department of Energy in the past.

NAKB/NDB are located at Rutgers University in the Institute for Quantitative Biomedicine, 174 Frelinghuysen Rd, Piscataway, NJ USA, 08854-8076

How to cite

Researchers who use the NDB should cite:

  • Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B (1992) The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. Biophys. J. 63, 751-759. DOI
  • Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM (2014) The Nucleic Acid Database: new features and capabilities. Nucleic Acids Res 42, D114-22. DOI

The history of NDB and plan for NAKB are described here:

  • Berman HM, Lawson CL, Schneider B (2022) Developing Community Resources for Nucleic Acid Structures. Life 12, 540. DOI

Contact us

Please send questions, comments, suggestions about NAKB to help@nakb.org.

Data Resources

NAKB is currently updated weekly on Thursdays, ~noon US ET (timing may change in future). Current update info is shown in the banner at the top of every page.

Resource Update FrequencyVersion
NAKB Annotationsweeklybanner date
RCSB PDB (API)weeklybanner date
Representative RNA Structure Setsweeklybanner version
DNATCOweeklybanner date
ONQUADROweeklybanner date
RNACentralsemiannualv22 2023-02-23
Rfamsemiannualv14.9 2022-11-15
3D FootPrintsemiannual2023-06-17
PANTHER Protein Classesv17.0 2022-02-23


NAKB Feature(s) Software
2D fold diagramsRNAview v.1.0
NA parameter tables, annotationsX3DNA-DSSR v.2.4
NA and Protein Sequence ClustersCD-HIT, CD-HIT-ESTv.4.8.1
template-based 2D fold viewerR2DTv.1.3
3D visualizationMol*